Query 009013
Match_columns 546
No_of_seqs 17 out of 19
Neff 2.5
Searched_HMMs 46136
Date Thu Mar 28 19:20:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10156 Med17: Subunit 17 of 99.9 9.1E-26 2E-30 231.6 4.6 277 3-342 162-463 (467)
2 COG4911 Uncharacterized conser 65.6 11 0.00025 34.9 4.7 57 436-501 45-107 (123)
3 PF13080 DUF3926: Protein of u 46.0 17 0.00036 28.9 2.1 27 427-454 2-28 (44)
4 KOG2714 SETA binding protein S 37.1 34 0.00073 37.9 3.5 61 40-116 84-147 (465)
5 COG4608 AppF ABC-type oligopep 36.8 28 0.00061 35.9 2.7 20 462-481 28-47 (268)
6 KOG4657 Uncharacterized conser 34.9 45 0.00099 34.3 3.8 44 457-500 151-195 (246)
7 COG1124 DppF ABC-type dipeptid 31.5 36 0.00077 35.1 2.5 19 463-481 23-41 (252)
8 PRK15337 type III secretion sy 27.2 33 0.00072 39.5 1.6 19 36-54 168-186 (686)
9 PRK05910 type III secretion sy 27.1 34 0.00074 38.8 1.6 19 36-54 163-181 (584)
10 TIGR01398 FlhA flagellar biosy 27.0 34 0.00074 39.3 1.6 20 35-54 161-180 (678)
11 PRK12792 flhA flagellar biosyn 26.8 35 0.00075 39.4 1.6 20 35-54 175-194 (694)
12 PF13715 DUF4480: Domain of un 24.4 86 0.0019 25.1 3.1 27 106-133 31-57 (88)
13 PRK06012 flhA flagellar biosyn 24.0 42 0.00091 38.6 1.6 20 35-54 178-197 (697)
14 cd07595 BAR_RhoGAP_Rich-like T 22.4 2E+02 0.0044 28.9 5.8 60 3-62 53-121 (244)
15 cd00025 BPI1 BPI/LBP/CETP N-te 21.8 6E+02 0.013 24.5 8.7 94 97-228 109-208 (223)
16 TIGR01399 hrcV type III secret 21.7 49 0.0011 38.1 1.6 20 35-54 157-176 (677)
17 PF00771 FHIPEP: FHIPEP family 21.2 32 0.00069 39.1 0.0 19 36-54 148-166 (658)
18 PF05233 PHB_acc: PHB accumula 20.7 1.9E+02 0.004 22.3 4.0 37 7-45 1-37 (41)
19 PRK12720 secretion system appa 20.4 54 0.0012 37.8 1.6 19 36-54 170-188 (675)
No 1
>PF10156 Med17: Subunit 17 of Mediator complex; InterPro: IPR019313 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med17 of the Mediator complex. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of Saccharomyces cerevisiae (Baker's yeast) lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3RJ1_B.
Probab=99.91 E-value=9.1e-26 Score=231.62 Aligned_cols=277 Identities=20% Similarity=0.252 Sum_probs=109.4
Q ss_pred CCCCCchhhhhhhhhhhhhhhhhhHHHHHHHHHhHHHHHHHHHHHhhhhHHHHHhhcc-cceeeeeecccCCC--CCceE
Q 009013 3 RPKALPNEVLSDLSVSAATKLQCYRHLGIYFKQSAKSLEQQIAKEARFYGALIRLQQN-WKVKRQRVAAPASG--NEGFT 79 (546)
Q Consensus 3 rPK~lPnE~lsDlAvsaAtKLq~yRhlg~YfKqSAKalEQQv~rEarFYGALiRLQqN-WKVKRQR~~a~~PG--neGF~ 79 (546)
.|.+.+.+.+.|.+|+.++|++++++.++|||++|+.||+||++|++||+.|+||+|| |+|+|. |. ...+.
T Consensus 162 ~~~~~~~~~~~~~~v~~g~K~~aL~~a~~~l~~aa~rL~~~v~~E~~yw~el~~lr~~gW~l~r~------~~~~~~~lg 235 (467)
T PF10156_consen 162 PPPKSESEQLDDAAVSIGWKLKALNKAADLLKQAAERLEKQVERETRYWSELLRLRQNGWRLFRM------PRKRQRSLG 235 (467)
T ss_dssp ---------SSHHHHTTTTTTTTTSSHHHHHHHHHHHHHTTHHHHHHHHHHTT---------------------------
T ss_pred CCCCchHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCeEEec------cCCCCceEE
Confidence 4556667777889999999999999999999999999999999999999999999999 999953 22 11133
Q ss_pred EEccCCCCCCCCCcc-CCCCCeee--------------------eeccCCCceeeeecCCCceeeEEEeeecccCCCCcc
Q 009013 80 IDLFDNSLYDSAPVS-RPSSLSTI--------------------RIDHDSAGMLAINLPPNSCRSFRFGFLGVQSGDSSK 138 (546)
Q Consensus 80 ~Dl~d~s~~D~~~~~-R~ssls~I--------------------~id~Ds~GmLav~vP~~~c~sL~~~f~g~~~~~~~k 138 (546)
+|++ ..|.+..+ |...+..+ +.+......|.|.|..+.|+.-...+.|.
T Consensus 236 v~~G---~~~ags~f~~~~g~a~lr~~~~~g~~~l~~~~~~~~~~~~~~~~~~lrV~I~~~~~~~~d~~~~g~------- 305 (467)
T PF10156_consen 236 VDYG---FREAGSEFRRDRGFAVLRRSDDTGSLELDPSSSLVSVPSDLKGRKFLRVRIQTKIEDEDDGILTGE------- 305 (467)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEec---CCCCCCccCCCCceeeeccCcccCCcccCcccccccCCccCCCceEEEEEEEeccccCCCCceecC-------
Confidence 3332 22333334 44444444 44444444555555555444444444441
Q ss_pred cccccccCCCCCCCcccccCCCchhhHHHHHHHHHHHHHHhhHHHHHHhHhhhhhc-ccCcceeecccchhhhhccccce
Q 009013 139 QCSKVKNSCSPRPSKEAKESVNDDECVREKHSLLREVHQAIFYEQVFDIVNREAFK-QSLGVNVTGIRENYLQLGIGLGI 217 (546)
Q Consensus 139 ~~e~~~~~~~~~p~~~~~~s~~d~e~vk~thslLR~ih~sIF~EQvFd~v~Reaf~-~s~g~nvtGi~E~~Lql~iGq~~ 217 (546)
..+ +.++.++.+..+..|++.|..||+|++|..++|||+. .+.|++|.+ |.+++.++++.
T Consensus 306 ----------s~~------~~~~~~~~~~~~~~l~~Ar~~lFeeELF~~L~REA~~L~s~~v~i~~---n~I~~~~~~~~ 366 (467)
T PF10156_consen 306 ----------SSL------PRSSKPDDSPIEKRLEEARNTLFEEELFYQLNREARQLISYGVRIRG---NKIIIELFPNE 366 (467)
T ss_dssp -----------------------------HHHHTTTTSTHHHHHHHHHHHHHHHHHHHS----SSS----------S-S-
T ss_pred ----------CCC------cccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEEc---CEEEEecCCCC
Confidence 000 1145678889999999999999999999999999995 456677766 99999999999
Q ss_pred eEEEEeecCCCCCCcccccccccccccccccccCCCccchhhhhhhhhcCCCCCCCchhHHHHHHHHHHHhhhcccCCcc
Q 009013 218 SIFLSLIPSNQGDLSVDSWVNQNVESGILPLDSHDGVKLAEEKDDILRKSGGYPNPLTYEIYLQQVFHEYLYGRAKNKPI 297 (546)
Q Consensus 218 sl~lsLv~s~q~~~~~~~~~~~~~~~a~L~l~t~dg~~~~~~~~~~~~~~~~~pN~~s~eIYLqq~Fhe~i~~k~~ek~~ 297 (546)
.+++.|++.+.++.+....... . .+..-.--..+|.+.|..+|..++..+.+--+.
T Consensus 367 ~l~ieLv~~~~~~~~~~~~~~~-~-----------------------~~~~a~~i~~~LrlLL~~~hr~nl~~r~~p~~~ 422 (467)
T PF10156_consen 367 KLEIELVSLDDDSSSNSSQESP-I-----------------------NDDLADLILHSLRLLLRHAHRQNLRRRSRPPPP 422 (467)
T ss_dssp -------S----GGGTSTTTTT-T-----------------------T-CTTCHHHHHHHHHHHHHHHHHHHHHHT----
T ss_pred EEEEEEecCCCCcccccccCCC-C-----------------------cchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 9999999888766433332000 0 000000011233334444444444444332222
Q ss_pred ccccccCCCCCCCCCCchhhhhhhhhhhhccchhhhhhhhhhcCc
Q 009013 298 STGTRVSGPPTKDGSGLLGHFCLSLAHRIFSNKVHVELENAVCGV 342 (546)
Q Consensus 298 ~~g~~~sg~~~~d~~gLL~HFc~slaHRifS~KV~~eLE~vV~~V 342 (546)
.+.+ .+......||..++.-+.|+++-.++...|++++..+
T Consensus 423 ~~~~----~~~~~~~~LLrpil~~~~H~~~~~~~~~~L~~~~~~l 463 (467)
T PF10156_consen 423 LTPR----KRPNPSPSLLRPILGYIRHENLVQRLESILDSLVREL 463 (467)
T ss_dssp ---------------------TTSTTTTTTSHHHHHHHHTTHHHH
T ss_pred cccc----ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2222 2356678999999999999999999999999988654
No 2
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=65.58 E-value=11 Score=34.90 Aligned_cols=57 Identities=32% Similarity=0.554 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhcceec------ceeeeEEEEecCCceEeEEEeeCCCCCCCceEEEEEeeccc
Q 009013 436 ILQQVASQVIRWLHEEALMVGIKAN------RDFLSLSFELDQGETVSLVAHVDPEDMRGCISWWLVMEDGF 501 (546)
Q Consensus 436 lLQQVAsqvI~WLheEA~~vG~ka~------RDFLcL~FeL~qge~l~LVAhvdP~d~~gCIsW~L~m~~~f 501 (546)
-+||++||+ .|+..|+.-+|+-.+ =||+++. ||+-+-|.=.+|-+| |-.|--|+.+|
T Consensus 45 ~l~e~e~q~-k~~l~~i~e~G~iird~d~glVDFpa~~----Ng~~~~lCWK~DE~~----imywH~~~EGF 107 (123)
T COG4911 45 ALQEYESQT-KKILDEIIEKGIIIRDIDIGLVDFPAII----NGKPAFLCWKIDEND----IMYWHYMDEGF 107 (123)
T ss_pred HHHHHHHHH-HHHHHHHHHcCceeeccccccccchhhh----CCceEEEEEecCCcc----eeeeecccccc
Confidence 489999995 788899999998542 2555544 899999988887654 78899998898
No 3
>PF13080 DUF3926: Protein of unknown function (DUF3926)
Probab=46.02 E-value=17 Score=28.89 Aligned_cols=27 Identities=41% Similarity=0.431 Sum_probs=22.5
Q ss_pred cCCCCchHHHHHHHHHHHHHHHHHHHhh
Q 009013 427 CDLADLPVIILQQVASQVIRWLHEEALM 454 (546)
Q Consensus 427 CdL~DLP~~lLQQVAsqvI~WLheEA~~ 454 (546)
|-|++||.=| ||-|.|++|-|.||-..
T Consensus 2 ~IleELP~Pi-qQsAkqmlnILQEELss 28 (44)
T PF13080_consen 2 HILEELPTPI-QQSAKQMLNILQEELSS 28 (44)
T ss_pred chHhhcCchH-HHHHHHHHHHHHHHHHh
Confidence 6688998865 88899999999999543
No 4
>KOG2714 consensus SETA binding protein SB1 and related proteins, contain BTB/POZ domain [General function prediction only]
Probab=37.11 E-value=34 Score=37.87 Aligned_cols=61 Identities=34% Similarity=0.416 Sum_probs=42.7
Q ss_pred HHHHHHHHhhhhH--HHH-HhhcccceeeeeecccCCCCCceEEEccCCCCCCCCCccCCCCCeeeeeccCCCceeeeec
Q 009013 40 LEQQIAKEARFYG--ALI-RLQQNWKVKRQRVAAPASGNEGFTIDLFDNSLYDSAPVSRPSSLSTIRIDHDSAGMLAINL 116 (546)
Q Consensus 40 lEQQv~rEarFYG--ALi-RLQqNWKVKRQR~~a~~PGneGF~~Dl~d~s~~D~~~~~R~ssls~I~id~Ds~GmLav~v 116 (546)
-||=.-+||+||| .|+ ||+-+|-- ||=+|.++-++....++-+.+.|+.-+--+|+...|-
T Consensus 84 ~~~llhdEA~fYGl~~llrrl~~~~~~----------------F~Gf~~~~s~~~~~~~~g~g~ai~~~~p~~~l~~AHg 147 (465)
T KOG2714|consen 84 PERLLHDEAMFYGLTPLLRRLTLCEEL----------------FDGFDLSLSRSVTGNAPGSGSAIRSAGPDVGLIVAHG 147 (465)
T ss_pred hhhhhhhhhhhcCcHHHHHHhhcCccc----------------ccccccccchhhccCCCCCCccccccCCCceEEEecc
Confidence 3555668999999 444 49988864 5555666666666677777788885555567776666
No 5
>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]
Probab=36.78 E-value=28 Score=35.89 Aligned_cols=20 Identities=35% Similarity=0.594 Sum_probs=17.1
Q ss_pred eeeeEEEEecCCceEeEEEe
Q 009013 462 DFLSLSFELDQGETVSLVAH 481 (546)
Q Consensus 462 DFLcL~FeL~qge~l~LVAh 481 (546)
-.=+++|++.+||++|||.-
T Consensus 28 avd~Vsf~i~~ge~~glVGE 47 (268)
T COG4608 28 AVDGVSFSIKEGETLGLVGE 47 (268)
T ss_pred EecceeEEEcCCCEEEEEec
Confidence 34579999999999999975
No 6
>KOG4657 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.91 E-value=45 Score=34.28 Aligned_cols=44 Identities=23% Similarity=0.427 Sum_probs=38.4
Q ss_pred ceecceeeeEEEEecCCceEeEEEe-eCCCCCCCceEEEEEeecc
Q 009013 457 IKANRDFLSLSFELDQGETVSLVAH-VDPEDMRGCISWWLVMEDG 500 (546)
Q Consensus 457 ~ka~RDFLcL~FeL~qge~l~LVAh-vdP~d~~gCIsW~L~m~~~ 500 (546)
++--+|+|||-.+=-.||.+-.|-. +||+|+.-|.|..+.+...
T Consensus 151 a~wy~dyLGleie~~hgevikfiFTnIdpkdp~~~FsF~vhL~e~ 195 (246)
T KOG4657|consen 151 ASWYNDYLGLEIEAGHGEVIKFIFTNIDPKDPTREFSFTVHLGED 195 (246)
T ss_pred HHHHHHhcCceeeeccCceEEEEEeccCCCCCccceeeEEeeccc
Confidence 3456899999999999999888765 9999999999999999855
No 7
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=31.50 E-value=36 Score=35.08 Aligned_cols=19 Identities=32% Similarity=0.676 Sum_probs=16.4
Q ss_pred eeeEEEEecCCceEeEEEe
Q 009013 463 FLSLSFELDQGETVSLVAH 481 (546)
Q Consensus 463 FLcL~FeL~qge~l~LVAh 481 (546)
+=.++|++.+||++|+|+-
T Consensus 23 l~~VS~~i~~Ge~lgivGe 41 (252)
T COG1124 23 LNNVSLEIERGETLGIVGE 41 (252)
T ss_pred hcceeEEecCCCEEEEEcC
Confidence 4578999999999999963
No 8
>PRK15337 type III secretion system protein InvA; Provisional
Probab=27.23 E-value=33 Score=39.46 Aligned_cols=19 Identities=21% Similarity=0.562 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHhhhhHHH
Q 009013 36 SAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 36 SAKalEQQv~rEarFYGAL 54 (546)
-||.--++++|||.||||.
T Consensus 168 eAr~RR~~l~~EadFyGAM 186 (686)
T PRK15337 168 GVKERRSVLERESQLYGSF 186 (686)
T ss_pred HHHHHHHHHHHHHHhccCc
Confidence 4788889999999999984
No 9
>PRK05910 type III secretion system protein; Validated
Probab=27.06 E-value=34 Score=38.78 Aligned_cols=19 Identities=16% Similarity=0.448 Sum_probs=16.6
Q ss_pred hHHHHHHHHHHHhhhhHHH
Q 009013 36 SAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 36 SAKalEQQv~rEarFYGAL 54 (546)
-||.--++++|||-||||.
T Consensus 163 eAr~RR~~l~~EadFyGAM 181 (584)
T PRK05910 163 RVSKQKNSLLEESDFFSAM 181 (584)
T ss_pred HHHHHHHHHHHHHHhcccc
Confidence 4788889999999999984
No 10
>TIGR01398 FlhA flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model.
Probab=26.98 E-value=34 Score=39.29 Aligned_cols=20 Identities=40% Similarity=0.763 Sum_probs=17.0
Q ss_pred HhHHHHHHHHHHHhhhhHHH
Q 009013 35 QSAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 35 qSAKalEQQv~rEarFYGAL 54 (546)
.-||.--++++|||-||||.
T Consensus 161 ~eAr~RR~~l~~Ea~FyGAM 180 (678)
T TIGR01398 161 EEAKKRREELEQEADFYGAM 180 (678)
T ss_pred HHHHHHHHHHHHHHHhcccc
Confidence 34788889999999999984
No 11
>PRK12792 flhA flagellar biosynthesis protein FlhA; Reviewed
Probab=26.76 E-value=35 Score=39.36 Aligned_cols=20 Identities=20% Similarity=0.625 Sum_probs=16.9
Q ss_pred HhHHHHHHHHHHHhhhhHHH
Q 009013 35 QSAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 35 qSAKalEQQv~rEarFYGAL 54 (546)
.-||.--++++|||-||||.
T Consensus 175 ~eAr~RR~~l~~Ea~FyGAM 194 (694)
T PRK12792 175 KEAQRRRRELEEESAFFGSM 194 (694)
T ss_pred HHHHHHHHHHHHHHhhcccc
Confidence 34788889999999999984
No 12
>PF13715 DUF4480: Domain of unknown function (DUF4480)
Probab=24.43 E-value=86 Score=25.09 Aligned_cols=27 Identities=22% Similarity=0.636 Sum_probs=23.3
Q ss_pred cCCCceeeeecCCCceeeEEEeeecccC
Q 009013 106 HDSAGMLAINLPPNSCRSFRFGFLGVQS 133 (546)
Q Consensus 106 ~Ds~GmLav~vP~~~c~sL~~~f~g~~~ 133 (546)
-|++|..++++|++. +.|.|.++|...
T Consensus 31 Td~~G~F~i~~~~g~-~~l~is~~Gy~~ 57 (88)
T PF13715_consen 31 TDENGRFSIKLPEGD-YTLKISYIGYET 57 (88)
T ss_pred ECCCeEEEEEEcCCC-eEEEEEEeCEEE
Confidence 489999999999877 789999999555
No 13
>PRK06012 flhA flagellar biosynthesis protein FlhA; Validated
Probab=24.01 E-value=42 Score=38.57 Aligned_cols=20 Identities=40% Similarity=0.757 Sum_probs=17.1
Q ss_pred HhHHHHHHHHHHHhhhhHHH
Q 009013 35 QSAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 35 qSAKalEQQv~rEarFYGAL 54 (546)
.-||.--++++|||-||||+
T Consensus 178 ~eAr~rR~~l~~Es~fyGaM 197 (697)
T PRK06012 178 EEAKKRRKELQQEADFYGAM 197 (697)
T ss_pred HHHHHHHHHHHHHHhhcccc
Confidence 34788889999999999984
No 14
>cd07595 BAR_RhoGAP_Rich-like The Bin/Amphiphysin/Rvs (BAR) domain of Rich-like Rho GTPase Activating Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to GAP interacting with CIP4 homologs proteins (Rich). Members contain an N-terminal BAR domain, followed by a Rho GAP domain, and a C-terminal prolin-rich region. Vertebrates harbor at least three Rho GAPs in this subfamily including Rich1, Rich2, and SH3-domain binding protein 1 (SH3BP1). Rich1 and Rich2 play complementary roles in the establishment and maintenance of cell polarity. Rich1 is a Cdc42- and Rac-specific GAP that binds to polarity proteins through the scaffold protein angiomotin and plays a role in maintaining the integrity of tight junctions. Rich2 is a Rac GAP that interacts with CD317 and plays a role in actin cytoskeleton organization and
Probab=22.38 E-value=2e+02 Score=28.93 Aligned_cols=60 Identities=18% Similarity=0.176 Sum_probs=49.0
Q ss_pred CCCCCchhhhhhhhhhhhhhh-------hhhHHHHHHHHHhHHHHHHHHH-HHhhhhHHHHHhh-cccc
Q 009013 3 RPKALPNEVLSDLSVSAATKL-------QCYRHLGIYFKQSAKSLEQQIA-KEARFYGALIRLQ-QNWK 62 (546)
Q Consensus 3 rPK~lPnE~lsDlAvsaAtKL-------q~yRhlg~YfKqSAKalEQQv~-rEarFYGALiRLQ-qNWK 62 (546)
|.|.+|.+.|++..+.++.-| +++...|...++-|.+..+|.. =|..|+-.|=+++ ..||
T Consensus 53 r~rk~p~~~Lg~~M~~~g~~l~~~s~lg~~L~~~g~a~~~ia~~~~~~d~~i~~~fl~pL~~~le~dik 121 (244)
T cd07595 53 RLKKLPEYGLAQSMLESSKELPDDSLLGKVLKLCGEAQNTLARELVDHEMNVEEDVLSPLQNILEVEIP 121 (244)
T ss_pred hhccCcHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456889999999998887766 5899999999999998777765 4789999998888 4663
No 15
>cd00025 BPI1 BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide.
Probab=21.78 E-value=6e+02 Score=24.53 Aligned_cols=94 Identities=17% Similarity=0.252 Sum_probs=66.0
Q ss_pred CCCeeeeeccCCCceeeeecCCCce--eeEEEeeecccCCCCcccccccccCCCCCCCcccccCCCchhhHHHHHHHHHH
Q 009013 97 SSLSTIRIDHDSAGMLAINLPPNSC--RSFRFGFLGVQSGDSSKQCSKVKNSCSPRPSKEAKESVNDDECVREKHSLLRE 174 (546)
Q Consensus 97 ssls~I~id~Ds~GmLav~vP~~~c--~sL~~~f~g~~~~~~~k~~e~~~~~~~~~p~~~~~~s~~d~e~vk~thslLR~ 174 (546)
+--..+++..|+.|.+.+.++.=.| .++++.|.| .+ .--...-+..+..
T Consensus 109 ~i~~~l~l~~d~~G~p~v~~~~C~~~v~~~~i~l~g---------------------------g~--~~l~~~f~~~i~~ 159 (223)
T cd00025 109 NIQADLRLGRDPSGRPKLSLSDCSSTVGSLRVHLGG---------------------------SL--GWLAKLFMNFIES 159 (223)
T ss_pred EEEEEEEEeeCCCCCeEEEeCCCCcccCcEEEEEeC---------------------------Ch--HHHHHHHHHHHHH
Confidence 4556889999999999999988776 889999998 11 1233555666666
Q ss_pred HHHHhhHHHHHHhHhhhhhcccCcceeecccchhhhh----ccccceeEEEEeecCCC
Q 009013 175 VHQAIFYEQVFDIVNREAFKQSLGVNVTGIRENYLQL----GIGLGISIFLSLIPSNQ 228 (546)
Q Consensus 175 ih~sIF~EQvFd~v~Reaf~~s~g~nvtGi~E~~Lql----~iGq~~sl~lsLv~s~q 228 (546)
-.+...++|+=.+++.. +...-+.+||| .+++.+.+-.+|+..-.
T Consensus 160 ~l~~~l~~~iCp~i~~~---------i~~~~~~~l~lp~~~~vd~~~~idysl~~~P~ 208 (223)
T cd00025 160 LLKKVLKGQLCPVIDAS---------LVSMLESLLQLPKLPPVDSNAGVDYSLTSPPV 208 (223)
T ss_pred HHHHHHHHHhhHHHHHH---------HHHhhhhhcCCceEeccCCcEEEEEEeecCCc
Confidence 66677777776666654 22234455554 57899999999987643
No 16
>TIGR01399 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane.
Probab=21.70 E-value=49 Score=38.10 Aligned_cols=20 Identities=30% Similarity=0.637 Sum_probs=16.8
Q ss_pred HhHHHHHHHHHHHhhhhHHH
Q 009013 35 QSAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 35 qSAKalEQQv~rEarFYGAL 54 (546)
.=||.--++++|||-||||+
T Consensus 157 ~eAr~RR~~l~~Ea~FyGAM 176 (677)
T TIGR01399 157 DEARRRRSTLEKESQLYGAM 176 (677)
T ss_pred HHHHHHHHHHHHHHHhccCc
Confidence 34788888999999999984
No 17
>PF00771 FHIPEP: FHIPEP family; InterPro: IPR001712 The Flagellar/Hr/Invasion Proteins Export Pore (FHIPEP) family [, ] consists of a number of proteins that constitute the type III secretion (or signal peptide-independent) pathway apparatus [, ]. This mechanism translocates proteins lacking an N-terminal signal peptide across the cell membrane in one step, as it does not require an intermediate periplasmic process to cleave the signal peptide. It is a common pathway amongst Gram-negative bacteria for secreting toxic and flagellar proteins. The pathway apparatus comprises three components: two within the inner membrane and one within the outer []. An FHIPEP protein is located within the inner membrane, although it is unknown which component it constitutes. FHIPEP proteins have all about 700 amino-acid residues. Within the sequence, the N terminus is highly conserved and hydrophobic, suggesting that this terminus is embedded within the membrane, with 6-8 transmembrane (TM) domains, while the C terminus is less conserved and appears to be devoid of TM regions. It is possible that members of the FHIPEP family serve as pores for the export of specific proteins.; GO: 0009306 protein secretion, 0016020 membrane; PDB: 3MIX_A 2X4A_A 3LW9_A 2X49_A 3MYD_A 3A5I_A.
Probab=21.18 E-value=32 Score=39.11 Aligned_cols=19 Identities=37% Similarity=0.781 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHhhhhHHH
Q 009013 36 SAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 36 SAKalEQQv~rEarFYGAL 54 (546)
-||.--++++|||-||||.
T Consensus 148 eA~~rR~~l~~E~~fyGaM 166 (658)
T PF00771_consen 148 EARRRREELEREADFYGAM 166 (658)
T ss_dssp -------------------
T ss_pred HHHHHHHHHHHHhhhhhhc
Confidence 4777788999999999995
No 18
>PF05233 PHB_acc: PHB accumulation regulatory domain; InterPro: IPR007897 The proteins this domain is found in are typically involved in regulating polymer accumulation in bacteria, for example the production of poly-beta-hydroxybutyrate (PHB) which is formed via the polymerisation of D(-)-3-hydroxybutyryl-CoA []. The function of this domain is unknown.
Probab=20.70 E-value=1.9e+02 Score=22.29 Aligned_cols=37 Identities=27% Similarity=0.392 Sum_probs=26.0
Q ss_pred CchhhhhhhhhhhhhhhhhhHHHHHHHHHhHHHHHHHHH
Q 009013 7 LPNEVLSDLSVSAATKLQCYRHLGIYFKQSAKSLEQQIA 45 (546)
Q Consensus 7 lPnE~lsDlAvsaAtKLq~yRhlg~YfKqSAKalEQQv~ 45 (546)
+|+|+|+++----..-.|.+ +|+|+.||-++|-++=+
T Consensus 1 l~~~~L~qlIrfyg~~mQ~~--m~~YLEqS~~~f~~~Q~ 37 (41)
T PF05233_consen 1 LPTEFLRQLIRFYGPSMQGM--MGSYLEQSMQMFAEMQE 37 (41)
T ss_pred CCHHHHHHHHHHcchhHHHH--HHHHHHHHHHHHHHHHH
Confidence 46777777755555555554 89999999999876543
No 19
>PRK12720 secretion system apparatus protein SsaV; Provisional
Probab=20.39 E-value=54 Score=37.79 Aligned_cols=19 Identities=42% Similarity=0.749 Sum_probs=16.3
Q ss_pred hHHHHHHHHHHHhhhhHHH
Q 009013 36 SAKSLEQQIAKEARFYGAL 54 (546)
Q Consensus 36 SAKalEQQv~rEarFYGAL 54 (546)
-||.=-++++|||-||||.
T Consensus 170 EAr~RR~~l~~EsdFyGAM 188 (675)
T PRK12720 170 EARRLRQHVQKESRLLGAM 188 (675)
T ss_pred HHHHHHHHHHHHHHhccCc
Confidence 4777788999999999984
Done!