MQM may be involved too. But there are other people as well. I think Lyari gang war is another significant factor. Also sectarian extremist parties. Example:
http://www.dailytimes.com.pk/default.asp?page=2010\07\03\story_3-7-2010_pg7_36
2 detained for targeted killing
KARACHI: The Nazimabad police on Friday arrested two people from Gulbahar for their involvement in the killing of a Shia writer and recovered a pistol from their possession. SHO Jhanzaib said that on a tip-off, the police party raided Petal Wali Gali located in Gulbahar area and arrested Shoaib, 26, and Nasir, 29. The SHO added that during initial course of investigation the culprits confessed killing Ayub Naqvi, a Shia writer in Nazimabad area. Police have registered an FIR and started investigations. The arrested culprits are residents of Petal Wali Gali. They are also associated with the defunct Sipah-e-Sahaba Pakistan. staff report
Those who know the Nazimabad area know very well that Peetal-wali-gali is an old hub of SSP.
http://www.dawn.com/wps/wcm/connect/dawn-content-library/dawn/the-newspaper/local/21-mqm-workers-booked-for-killing-policemen-370-sk-05
MQM workers booked for killing policemen
KARACHI: Workers of the Muttahida Qaumi Movement have been booked in the murder case of a police officer and his armed guard who were ambushed in a Lines Area locality on Thursday evening, officials said on Friday.
http://www.samaa.tv/News22192-Four_suspects_arrested_in_Karachi.aspx
KARACHI: The police on Saturday apprehended four suspects, including an activist of a banned religious outfit, allegedly involved in ongoing spree of target killings in Karachi.
According to police, they raided a house in Machhar Colony and arrested three accused, Muhammad Ayub, Noor Islam and Bilal, besides recovering cache of arms from their possession.
The arrested men have admitted killing Abdul Aziz, member of an outlawed organization.
Acting on a tip off, a special team of rangers captured a suspected terrorist namely Abu Huraira, who is believed to be a member of banned Lashkar-e-Jhangvi.
The accused is being interrogated for his involvement in ongoing incidents of target killings. SAMAA