Query psy11983
Match_columns 66
No_of_seqs 82 out of 84
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 15:38:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2037|consensus 97.9 3E-05 6.4E-10 62.3 5.4 43 2-44 489-531 (552)
2 PF06842 DUF1242: Protein of u 80.1 1.4 3.1E-05 24.2 1.6 16 2-17 3-18 (36)
3 PF01066 CDP-OH_P_transf: CDP- 67.3 6.9 0.00015 23.8 2.7 26 14-39 50-75 (101)
4 cd01324 cbb3_Oxidase_CcoQ Cyto 63.9 3.4 7.4E-05 23.4 0.7 22 2-23 20-42 (48)
5 PF12841 YvrJ: YvrJ protein fa 59.4 12 0.00027 20.5 2.4 28 6-33 10-37 (38)
6 PF05545 FixQ: Cbb3-type cytoc 57.2 5.8 0.00013 21.9 0.9 16 2-17 19-34 (49)
7 PF01277 Oleosin: Oleosin; In 51.4 16 0.00035 24.5 2.5 35 2-36 68-102 (118)
8 PF13974 YebO: YebO-like prote 47.3 56 0.0012 20.7 4.3 34 2-35 6-40 (80)
9 TIGR00560 pgsA CDP-diacylglyce 46.3 21 0.00046 24.7 2.5 24 14-37 54-77 (182)
10 PRK10174 hypothetical protein; 45.4 51 0.0011 20.8 3.9 28 9-38 12-46 (75)
11 PRK10832 phosphatidylglyceroph 44.0 20 0.00043 25.0 2.1 22 14-35 53-74 (182)
12 KOG2612|consensus 43.9 48 0.001 22.0 3.8 28 25-52 6-33 (103)
13 PF10828 DUF2570: Protein of u 42.0 70 0.0015 20.3 4.2 36 2-37 8-44 (110)
14 TIGR00473 pssA CDP-diacylglyce 38.2 29 0.00062 23.5 2.1 23 14-36 41-63 (151)
15 PF06240 COXG: Carbon monoxide 35.0 67 0.0014 20.4 3.4 29 17-45 109-138 (140)
16 PHA03283 envelope glycoprotein 33.6 16 0.00034 30.3 0.3 17 2-18 411-427 (542)
17 cd07307 BAR The Bin/Amphiphysi 33.5 1.1E+02 0.0023 18.8 4.1 34 13-46 56-89 (194)
18 KOG4320|consensus 32.4 35 0.00076 25.8 2.0 24 4-28 59-82 (253)
19 PF08397 IMD: IRSp53/MIM homol 32.1 87 0.0019 21.8 3.8 33 14-46 61-93 (219)
20 KOG3808|consensus 31.5 34 0.00074 21.5 1.5 18 3-20 13-30 (74)
21 PF13993 YccJ: YccJ-like prote 31.2 1E+02 0.0023 19.1 3.6 28 9-38 6-40 (69)
22 PF04341 DUF485: Protein of un 30.5 69 0.0015 19.7 2.8 16 4-19 64-79 (91)
23 TIGR00847 ccoS cytochrome oxid 29.3 52 0.0011 19.1 2.0 23 3-25 12-36 (51)
24 COG4650 RtcR Sigma54-dependent 28.8 43 0.00094 27.1 2.0 21 13-33 405-425 (531)
25 COG4904 Uncharacterized protei 27.5 94 0.002 22.4 3.3 23 25-47 58-80 (174)
26 PLN02558 CDP-diacylglycerol-gl 27.3 52 0.0011 23.4 2.0 23 15-37 60-82 (203)
27 PF10753 DUF2566: Protein of u 26.0 84 0.0018 18.7 2.5 26 2-27 12-37 (55)
28 PRK04366 glycine dehydrogenase 25.4 1.6E+02 0.0034 22.7 4.5 36 4-39 329-366 (481)
29 COG0811 TolQ Biopolymer transp 24.6 1.5E+02 0.0033 20.8 4.0 37 2-38 173-209 (216)
30 PF03589 Antiterm: Antitermina 22.9 1.9E+02 0.0042 18.2 3.9 35 20-54 52-86 (95)
31 PF10823 DUF2568: Protein of u 22.3 1.8E+02 0.0038 18.4 3.6 44 3-46 10-54 (93)
32 PF03597 CcoS: Cytochrome oxid 21.5 68 0.0015 18.0 1.4 10 15-24 25-34 (45)
33 PF15182 OTOS: Otospiralin 21.0 1.2E+02 0.0026 18.9 2.5 24 10-36 27-52 (69)
34 KOG1782|consensus 20.7 76 0.0017 21.9 1.8 19 25-43 37-55 (129)
35 PHA00450 host dGTPase inhibito 20.5 76 0.0017 20.5 1.6 17 16-32 5-21 (85)
No 1
>KOG2037|consensus
Probab=97.86 E-value=3e-05 Score=62.34 Aligned_cols=43 Identities=19% Similarity=0.341 Sum_probs=39.5
Q ss_pred hhHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHHHHHHHHHH
Q psy11983 2 GCALLTLITWAYIRYSGEMTDIGIKIDDVANTVWDNRLVKLNQ 44 (66)
Q Consensus 2 gl~L~~L~~WaYiRYSG~~revG~~ID~~A~~lwe~~l~p~~~ 44 (66)
+.++..+++|+|++|||++|+++..+|+.+..+||++.++-..
T Consensus 489 ~q~~~~~~~~a~~~~s~~~~~l~~~v~~~~~~l~e~~~~~~~~ 531 (552)
T KOG2037|consen 489 KQLVEELETWAYVLLSEQERTLAHKVKSQEKLLWEGFSKESRE 531 (552)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhchhhh
Confidence 4567789999999999999999999999999999999987776
No 2
>PF06842 DUF1242: Protein of unknown function (DUF1242); InterPro: IPR009653 This family consists of a number of eukaryotic proteins of around 72 residues in length. The function of this family is unknown.
Probab=80.06 E-value=1.4 Score=24.20 Aligned_cols=16 Identities=38% Similarity=0.447 Sum_probs=13.4
Q ss_pred hhHHHHHHHHHHHhhc
Q psy11983 2 GCALLTLITWAYIRYS 17 (66)
Q Consensus 2 gl~L~~L~~WaYiRYS 17 (66)
.+.|+.+||.+|+|..
T Consensus 3 ~ViLL~ICTCtYir~~ 18 (36)
T PF06842_consen 3 TVILLLICTCTYIRSI 18 (36)
T ss_pred hhHHHHHHHhHhHHhH
Confidence 4678999999999864
No 3
>PF01066 CDP-OH_P_transf: CDP-alcohol phosphatidyltransferase; InterPro: IPR000462 A number of phosphatidyltransferases, which are all involved in phospholipid biosynthesis and that share the property of catalyzing the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond share a conserved sequence region [, ]. These enzymes are proteins of 200 to 400 amino acid residues. The conserved region contains three aspartic acid residues and is located in the N-terminal section of the sequences.; GO: 0016780 phosphotransferase activity, for other substituted phosphate groups, 0008654 phospholipid biosynthetic process, 0016020 membrane
Probab=67.30 E-value=6.9 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.263 Sum_probs=23.1
Q ss_pred HhhccchhhHHHHHHHHHHHHHHHHH
Q psy11983 14 IRYSGEMTDIGIKIDDVANTVWDNRL 39 (66)
Q Consensus 14 iRYSG~~revG~~ID~~A~~lwe~~l 39 (66)
-|.+|+-+++|..+|.+++.+-+-+.
T Consensus 50 AR~~~~~S~~G~~lD~~~D~i~~~~~ 75 (101)
T PF01066_consen 50 ARRRNQSSPFGAYLDSVADRISFVAL 75 (101)
T ss_pred HHHcCCCCchHHHHhHHhHHHHHHHH
Confidence 48899999999999999999887755
No 4
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=63.92 E-value=3.4 Score=23.43 Aligned_cols=22 Identities=14% Similarity=0.389 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHHHh-hccchhhH
Q psy11983 2 GCALLTLITWAYIR-YSGEMTDI 23 (66)
Q Consensus 2 gl~L~~L~~WaYiR-YSG~~rev 23 (66)
.+.+++++.|+|.+ -..++.|.
T Consensus 20 ~~~Figiv~wa~~p~~k~~f~ea 42 (48)
T cd01324 20 ALFFLGVVVWAFRPGRKKAFDEA 42 (48)
T ss_pred HHHHHHHHHHHhCCCcchhHHHH
Confidence 46788999999983 33444443
No 5
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=59.38 E-value=12 Score=20.51 Aligned_cols=28 Identities=7% Similarity=0.382 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhccchhhHHHHHHHHHHH
Q psy11983 6 LTLITWAYIRYSGEMTDIGIKIDDVANT 33 (66)
Q Consensus 6 ~~L~~WaYiRYSG~~revG~~ID~~A~~ 33 (66)
++++.+.-+|..+++.++..+|.++.+.
T Consensus 10 i~va~yLL~R~E~kld~L~~~i~~L~~~ 37 (38)
T PF12841_consen 10 IAVAIYLLVRIEKKLDELTESINELSEA 37 (38)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4677788899999999999999988764
No 6
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=57.24 E-value=5.8 Score=21.91 Aligned_cols=16 Identities=19% Similarity=0.453 Sum_probs=12.6
Q ss_pred hhHHHHHHHHHHHhhc
Q psy11983 2 GCALLTLITWAYIRYS 17 (66)
Q Consensus 2 gl~L~~L~~WaYiRYS 17 (66)
.+++++++.|+|.+-+
T Consensus 19 ~~~F~gi~~w~~~~~~ 34 (49)
T PF05545_consen 19 FVFFIGIVIWAYRPRN 34 (49)
T ss_pred HHHHHHHHHHHHcccc
Confidence 4678899999998653
No 7
>PF01277 Oleosin: Oleosin; InterPro: IPR000136 Oleosins [] are the proteinaceous components of plants' lipid storage bodies called oil bodies. Oil bodies are small droplets (0.2 to 1.5 mu-m in diameter) containing mostly triacylglycerol that are surrounded by a phospholipid/ oleosin annulus. Oleosins may have a structural role in stabilising the lipid body during dessication of the seed, by preventing coalescence of the oil. They may also provide recognition signals for specific lipase anchorage in lipolysis during seedling growth. Oleosins are found in the monolayer lipid/ water interface of oil bodies and probably interact with both the lipid and phospholipid moieties. Oleosins are proteins of 16 Kd to 24 Kd and are composed of three domains: an N-terminal hydrophilic region of variable length (from 30 to 60 residues); a central hydrophobic domain of about 70 residues and a C-terminal amphipathic region of variable length (from 60 to 100 residues). The central hydrophobic domain is proposed to be made up of beta-strand structure and to interact with the lipids []. It is the only domain whose sequence is conserved.; GO: 0012511 monolayer-surrounded lipid storage body, 0016021 integral to membrane
Probab=51.38 E-value=16 Score=24.52 Aligned_cols=35 Identities=20% Similarity=0.375 Sum_probs=27.6
Q ss_pred hhHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHH
Q psy11983 2 GCALLTLITWAYIRYSGEMTDIGIKIDDVANTVWD 36 (66)
Q Consensus 2 gl~L~~L~~WaYiRYSG~~revG~~ID~~A~~lwe 36 (66)
|++-++...|.|-.+.|....-...+|..-..+=|
T Consensus 68 g~~~ls~lsW~~~y~rg~~~~~~~q~d~Ak~ri~d 102 (118)
T PF01277_consen 68 GLTALSSLSWMYNYFRGRHPPGPDQLDYAKRRIAD 102 (118)
T ss_pred HHHHHHHHHHHHHHhccCCCCCCccHHHHHHHHHH
Confidence 56778999999999999987777777776655544
No 8
>PF13974 YebO: YebO-like protein
Probab=47.26 E-value=56 Score=20.69 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHHH-hhccchhhHHHHHHHHHHHHH
Q psy11983 2 GCALLTLITWAYI-RYSGEMTDIGIKIDDVANTVW 35 (66)
Q Consensus 2 gl~L~~L~~WaYi-RYSG~~revG~~ID~~A~~lw 35 (66)
.+++++|.+|-|+ |+|=+--|-=..+..+++--=
T Consensus 6 ~~~lv~livWFFVnRaSvRANEQI~LL~~ileqQK 40 (80)
T PF13974_consen 6 LVLLVGLIVWFFVNRASVRANEQIELLEEILEQQK 40 (80)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 3578999999997 888887666555555555433
No 9
>TIGR00560 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase. Alternate names: phosphatidylglycerophosphate synthase; glycerophosphate phosphatidyltransferase; PGP synthase. A number of related enzymes are quite similar in both sequence and catalytic activity, including Saccharamyces cerevisiae YDL142c, now known to be a cardiolipin synthase. There may be problems with incorrect transitive annotation of near homologs as authentic CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase.
Probab=46.32 E-value=21 Score=24.71 Aligned_cols=24 Identities=21% Similarity=0.254 Sum_probs=21.5
Q ss_pred HhhccchhhHHHHHHHHHHHHHHH
Q psy11983 14 IRYSGEMTDIGIKIDDVANTVWDN 37 (66)
Q Consensus 14 iRYSG~~revG~~ID~~A~~lwe~ 37 (66)
-|..++-.++|..+|-+||.+..-
T Consensus 54 AR~~~~~S~~G~~LDp~aDk~~~~ 77 (182)
T TIGR00560 54 ARKWNQVSNFGKFLDPLADKVLVL 77 (182)
T ss_pred HHHcCCCChHHHHHHHHhhHHHHH
Confidence 488899999999999999998865
No 10
>PRK10174 hypothetical protein; Provisional
Probab=45.37 E-value=51 Score=20.79 Aligned_cols=28 Identities=29% Similarity=0.610 Sum_probs=20.7
Q ss_pred HHHHHHhhccchhhHHHHHHHH-------HHHHHHHH
Q psy11983 9 ITWAYIRYSGEMTDIGIKIDDV-------ANTVWDNR 38 (66)
Q Consensus 9 ~~WaYiRYSG~~revG~~ID~~-------A~~lwe~~ 38 (66)
.-||-+|-+- .|+..+|.++ |+.||++=
T Consensus 12 ~eWA~vR~TS--~EIAeAIFE~A~~dE~lAe~IWeeG 46 (75)
T PRK10174 12 GEWASLRNTS--PEIAEAIFEVAGYDEKLAEKIWEEG 46 (75)
T ss_pred HHHHHHhhCC--HHHHHHHHHHhcccHHHHHHHHHhc
Confidence 4588888664 6788888765 67899883
No 11
>PRK10832 phosphatidylglycerophosphate synthetase; Provisional
Probab=44.00 E-value=20 Score=24.98 Aligned_cols=22 Identities=32% Similarity=0.342 Sum_probs=19.9
Q ss_pred HhhccchhhHHHHHHHHHHHHH
Q psy11983 14 IRYSGEMTDIGIKIDDVANTVW 35 (66)
Q Consensus 14 iRYSG~~revG~~ID~~A~~lw 35 (66)
-|..|+-.++|..+|-+||.+-
T Consensus 53 AR~~~~~S~lG~~LDPlADKll 74 (182)
T PRK10832 53 ARRWNQSTRFGAFLDPVADKVM 74 (182)
T ss_pred HHHcCCCChHHHHHhHHHHHHH
Confidence 3888999999999999999986
No 12
>KOG2612|consensus
Probab=43.90 E-value=48 Score=21.97 Aligned_cols=28 Identities=32% Similarity=0.322 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy11983 25 IKIDDVANTVWDNRLVKLNQDFKEVTVR 52 (66)
Q Consensus 25 ~~ID~~A~~lwe~~l~p~~~~~~~~~~~ 52 (66)
.-||++|+.+.++.+.-+.+..+....+
T Consensus 6 iniDe~aNgilnnLL~~~iqdI~a~e~~ 33 (103)
T KOG2612|consen 6 INIDEAANGILNNLLDDAIQDIFAEEHH 33 (103)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999998888877755443
No 13
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=41.96 E-value=70 Score=20.28 Aligned_cols=36 Identities=17% Similarity=0.223 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHHhhcc-chhhHHHHHHHHHHHHHHH
Q psy11983 2 GCALLTLITWAYIRYSG-EMTDIGIKIDDVANTVWDN 37 (66)
Q Consensus 2 gl~L~~L~~WaYiRYSG-~~revG~~ID~~A~~lwe~ 37 (66)
+++++.+++|++++|.. ....+-..-+..+..+=++
T Consensus 8 ~l~~lvl~L~~~l~~qs~~i~~L~a~n~~q~~tI~qq 44 (110)
T PF10828_consen 8 ALAVLVLGLGGWLWYQSQRIDRLRAENKAQAQTIQQQ 44 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666667777776643 3444555555555555433
No 14
>TIGR00473 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase. This enzyme, CDP-diacylglycerol--serine O-phosphatidyltransferase, is involved in phospholipid biosynthesis catalyzing the reaction CDP-diacylglycerol + L-serine = CMP + L-1-phosphatidylserine. Members of this family do not bear any significant sequence similarity to the corresponding E.coli protein.
Probab=38.22 E-value=29 Score=23.51 Aligned_cols=23 Identities=26% Similarity=0.416 Sum_probs=19.4
Q ss_pred HhhccchhhHHHHHHHHHHHHHH
Q psy11983 14 IRYSGEMTDIGIKIDDVANTVWD 36 (66)
Q Consensus 14 iRYSG~~revG~~ID~~A~~lwe 36 (66)
-|..|.-++.|..+|.+++.+=-
T Consensus 41 AR~~~~~s~~G~~lDsl~D~vsf 63 (151)
T TIGR00473 41 ARKTNRVSDFGKELDSLADVVSF 63 (151)
T ss_pred HHHcCCCChHHHHHHHHHHHHHH
Confidence 47778889999999999998743
No 15
>PF06240 COXG: Carbon monoxide dehydrogenase subunit G (CoxG); InterPro: IPR010419 The CO dehydrogenase structural genes coxMSL are flanked by nine accessory genes arranged as the cox gene cluster. The cox genes are specifically and coordinately transcribed under chemolithoautotrophic conditions in the presence of CO as carbon and energy source [].; PDB: 2NS9_A 2PCS_A.
Probab=35.05 E-value=67 Score=20.39 Aligned_cols=29 Identities=21% Similarity=0.420 Sum_probs=20.1
Q ss_pred ccchhhHH-HHHHHHHHHHHHHHHHHHHHH
Q psy11983 17 SGEMTDIG-IKIDDVANTVWDNRLVKLNQD 45 (66)
Q Consensus 17 SG~~revG-~~ID~~A~~lwe~~l~p~~~~ 45 (66)
+|.+..+| ..|+.+|+.+.++|.+.+-+.
T Consensus 109 ~G~la~~g~~~i~~~~~~l~~~f~~~l~~~ 138 (140)
T PF06240_consen 109 GGPLASLGQRLIESVARRLIEQFFENLERK 138 (140)
T ss_dssp ECHHHHC-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCHHHhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 45555665 578888888888888766554
No 16
>PHA03283 envelope glycoprotein E; Provisional
Probab=33.60 E-value=16 Score=30.25 Aligned_cols=17 Identities=29% Similarity=0.704 Sum_probs=14.4
Q ss_pred hhHHHHHHHHHHHhhcc
Q psy11983 2 GCALLTLITWAYIRYSG 18 (66)
Q Consensus 2 gl~L~~L~~WaYiRYSG 18 (66)
++++++|.+|+++||-+
T Consensus 411 ~~~~~~l~vw~c~~~r~ 427 (542)
T PHA03283 411 AALLVALVVWGCILYRR 427 (542)
T ss_pred HHHHHHHhhhheeeehh
Confidence 67899999999999743
No 17
>cd07307 BAR The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-
Probab=33.46 E-value=1.1e+02 Score=18.84 Aligned_cols=34 Identities=6% Similarity=0.098 Sum_probs=27.3
Q ss_pred HHhhccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy11983 13 YIRYSGEMTDIGIKIDDVANTVWDNRLVKLNQDF 46 (66)
Q Consensus 13 YiRYSG~~revG~~ID~~A~~lwe~~l~p~~~~~ 46 (66)
..+++.-+++++...++..+.+.+.+++|+.+..
T Consensus 56 l~~~~~~~~~l~~~~~~~~~~~~~~v~~pL~~~~ 89 (194)
T cd07307 56 LEKFGKIQKELEEFRDQLEQKLENKVIEPLKEYL 89 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677788888888888888888999988766
No 18
>KOG4320|consensus
Probab=32.44 E-value=35 Score=25.82 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHhhccchhhHHHHHH
Q psy11983 4 ALLTLITWAYIRYSGEMTDIGIKID 28 (66)
Q Consensus 4 ~L~~L~~WaYiRYSG~~revG~~ID 28 (66)
..+.+.+|+|+|| +|.+|+-..=|
T Consensus 59 ~~vll~l~~yvRY-rQl~~~~~h~~ 82 (253)
T KOG4320|consen 59 GAVLLALIIYVRY-RQLLELFRHAN 82 (253)
T ss_pred HHHHHHHHHHHHH-HHHHHHHhhcc
Confidence 4577889999999 56766665555
No 19
>PF08397 IMD: IRSp53/MIM homology domain; InterPro: IPR013606 The IMD (IRSp53 and MIM (missing in metastases) homology) domain is a BAR-like domain of approximately 250 amino acids found at the N-terminal in the insulin receptor tyrosine kinase substrate p53 (IRSp53) and in the evolutionarily related IRSp53/MIM family. In IRSp53, a ubiquitous regulator o the actin cytoskeleton, the IMD domain acts as conserved F-actin bundling domain involved in filopodium formation. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 (Rho-family GTPases) and is SH3-independent [, , ]. The IRSp53/MIM family is a novel F-actin bundling protein family that includes invertebrate relatives: Vertebrate MIM (missing in metastasis), an actin-binding scaffold protein that may be involved in cancer metastasis. Vertebrate ABBA-1, a MIM-related protein. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) or insulin receptor tyrosine kinase substrate p53 (IRSp53), a multifunctional adaptor protein that links Rac1 with a Wiskott-Aldrich syndrome family verprolin-homologous protein 2 (WAVE2) to induce lamellipodia or Cdc42 with Mena to induce filopodia []. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2-like proteins 1 and 2 (BAI1-associated protein 2-like proteins 1 and 2). Drosophila melanogaster (Fruit fly) CG32082-PA. Caenorhabditis elegans M04F3.5 protein. The vertebrate IRSp53/MIM family is divided into two major groups: the IRSp53 subfamily and the MIM/ABBA subfamily. The putative invertebrate homologues are positioned between them. The IRSp53 subfamily members contain an SH3 domain, and the MIM/ABBA subfamily proteins contain a WH2 (WASP-homology 2) domain. The vertebrate SH3-containing subfamily is further divided into three groups according to the presence or absence of the WWB and the half-CRIB motif. The IMD domain can bind to and bundle actin filaments, bind to membranes and interact with the small GTPase Rac [, ]. The IMD domain folds as a coiled coil of three extended alpha-helices and a shorter C-terminal helix. Helix 4 packs tightly against the other three helices, and thus represents an integral part of the domain. The fold of the IMD domain closely resembles that of the BAR (Bin-Amphiphysin-RVS) domain, a functional module serving both as a sensor and inducer of membrane curvature []. The WH2 domain performs a scaffolding function [].; GO: 0008093 cytoskeletal adaptor activity, 0017124 SH3 domain binding, 0007165 signal transduction, 0046847 filopodium assembly; PDB: 2D1L_A 3OK8_B 1WDZ_B 1Y2O_A 2YKT_A.
Probab=32.11 E-value=87 Score=21.75 Aligned_cols=33 Identities=12% Similarity=0.218 Sum_probs=22.7
Q ss_pred HhhccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy11983 14 IRYSGEMTDIGIKIDDVANTVWDNRLVKLNQDF 46 (66)
Q Consensus 14 iRYSG~~revG~~ID~~A~~lwe~~l~p~~~~~ 46 (66)
.|.|+.+|.+....+.+...+-+.++.|+-+.+
T Consensus 61 ~~~s~~~r~i~~~~~~~~~~~~~~li~pLe~~~ 93 (219)
T PF08397_consen 61 MQISEVHRRIENELEEVFKAFHSELIQPLEKKL 93 (219)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667777777777777777777777776554
No 20
>KOG3808|consensus
Probab=31.48 E-value=34 Score=21.50 Aligned_cols=18 Identities=28% Similarity=0.397 Sum_probs=13.5
Q ss_pred hHHHHHHHHHHHhhccch
Q psy11983 3 CALLTLITWAYIRYSGEM 20 (66)
Q Consensus 3 l~L~~L~~WaYiRYSG~~ 20 (66)
.+|+-+||.||.|---++
T Consensus 13 ~~LLfiCTCAYlk~vpr~ 30 (74)
T KOG3808|consen 13 VILLFICTCAYLKSVPRF 30 (74)
T ss_pred HHHHHHHHHHHHhhcccc
Confidence 568889999999754333
No 21
>PF13993 YccJ: YccJ-like protein
Probab=31.25 E-value=1e+02 Score=19.12 Aligned_cols=28 Identities=25% Similarity=0.577 Sum_probs=20.4
Q ss_pred HHHHHHhhccchhhHHHHHHHH-------HHHHHHHH
Q psy11983 9 ITWAYIRYSGEMTDIGIKIDDV-------ANTVWDNR 38 (66)
Q Consensus 9 ~~WaYiRYSG~~revG~~ID~~-------A~~lwe~~ 38 (66)
.-||-+|-+- .|+..+|.++ |+.|||+=
T Consensus 6 ~eWA~~ReTS--~EIAeAIFElA~~dE~lAekIWeeG 40 (69)
T PF13993_consen 6 GEWANVRETS--IEIAEAIFELANNDEVLAEKIWEEG 40 (69)
T ss_pred HHHHHHhcCC--HHHHHHHHHHhcccHHHHHHHHHcc
Confidence 4588887664 5788888765 57899883
No 22
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=30.49 E-value=69 Score=19.67 Aligned_cols=16 Identities=25% Similarity=0.692 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHhhccc
Q psy11983 4 ALLTLITWAYIRYSGE 19 (66)
Q Consensus 4 ~L~~L~~WaYiRYSG~ 19 (66)
++.-..+|.|+|...+
T Consensus 64 ~~~~~l~~~Yv~~An~ 79 (91)
T PF04341_consen 64 VFAWVLTWLYVRRANR 79 (91)
T ss_pred HHHHHHHHHHHHHHcc
Confidence 3445678999998776
No 23
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=29.31 E-value=52 Score=19.06 Aligned_cols=23 Identities=22% Similarity=0.121 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHHhh--ccchhhHHH
Q psy11983 3 CALLTLITWAYIRY--SGEMTDIGI 25 (66)
Q Consensus 3 l~L~~L~~WaYiRY--SG~~revG~ 25 (66)
+.++.+++|+++-- ||||.+.-+
T Consensus 12 l~l~~~~l~~f~Wavk~GQfDDle~ 36 (51)
T TIGR00847 12 LLLGGVGLVAFLWSLKSGQYDDLKG 36 (51)
T ss_pred HHHHHHHHHHHHHHHccCCCCCCcc
Confidence 34445555555544 899987654
No 24
>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]
Probab=28.78 E-value=43 Score=27.15 Aligned_cols=21 Identities=10% Similarity=0.340 Sum_probs=17.5
Q ss_pred HHhhccchhhHHHHHHHHHHH
Q psy11983 13 YIRYSGEMTDIGIKIDDVANT 33 (66)
Q Consensus 13 YiRYSG~~revG~~ID~~A~~ 33 (66)
--|++|+|||+...+-..|..
T Consensus 405 qa~w~gnfrelsasvtrmatl 425 (531)
T COG4650 405 QATWRGNFRELSASVTRMATL 425 (531)
T ss_pred chhhcccHHHHhHHHHHHHHH
Confidence 357899999999999888754
No 25
>COG4904 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.49 E-value=94 Score=22.37 Aligned_cols=23 Identities=13% Similarity=0.430 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy11983 25 IKIDDVANTVWDNRLVKLNQDFK 47 (66)
Q Consensus 25 ~~ID~~A~~lwe~~l~p~~~~~~ 47 (66)
+-+|+++..+|+.+++.+|+.+.
T Consensus 58 kDl~k~~~~v~~k~~~~FYEnyG 80 (174)
T COG4904 58 KDLTKAAKLVWRKTVEAFYENYG 80 (174)
T ss_pred hhhHHHHHHHHHHHHHHHHHHcC
Confidence 56789999999999999999775
No 26
>PLN02558 CDP-diacylglycerol-glycerol-3-phosphate/ 3-phosphatidyltransferase
Probab=27.29 E-value=52 Score=23.41 Aligned_cols=23 Identities=26% Similarity=0.176 Sum_probs=20.3
Q ss_pred hhccchhhHHHHHHHHHHHHHHH
Q psy11983 15 RYSGEMTDIGIKIDDVANTVWDN 37 (66)
Q Consensus 15 RYSG~~revG~~ID~~A~~lwe~ 37 (66)
|-.++-.++|..+|-+||.+-.-
T Consensus 60 R~~n~~T~~G~~lDPiaDKll~~ 82 (203)
T PLN02558 60 RKMKLGTAFGAFLDPVADKLMVA 82 (203)
T ss_pred HHcCCCChHHHHHhHHHHHHHHH
Confidence 77799999999999999998754
No 27
>PF10753 DUF2566: Protein of unknown function (DUF2566); InterPro: IPR019689 This entry is represented by Pseudomonas phage PaP3, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.02 E-value=84 Score=18.73 Aligned_cols=26 Identities=19% Similarity=0.232 Sum_probs=21.7
Q ss_pred hhHHHHHHHHHHHhhccchhhHHHHH
Q psy11983 2 GCALLTLITWAYIRYSGEMTDIGIKI 27 (66)
Q Consensus 2 gl~L~~L~~WaYiRYSG~~revG~~I 27 (66)
|.++-++.||.-+|=|...|.+...+
T Consensus 12 g~~is~~iT~flskDs~~iRllsa~l 37 (55)
T PF10753_consen 12 GAVISALITFFLSKDSLRIRLLSAIL 37 (55)
T ss_pred HHHHHHHHHHHHhcchhHHHHHHHHH
Confidence 56778899999999999999887654
No 28
>PRK04366 glycine dehydrogenase subunit 2; Validated
Probab=25.37 E-value=1.6e+02 Score=22.74 Aligned_cols=36 Identities=19% Similarity=0.135 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhhccc--hhhHHHHHHHHHHHHHHHHH
Q psy11983 4 ALLTLITWAYIRYSGE--MTDIGIKIDDVANTVWDNRL 39 (66)
Q Consensus 4 ~L~~L~~WaYiRYSG~--~revG~~ID~~A~~lwe~~l 39 (66)
++.++..|.|.++-|. ++++...+=+.|..+++.+.
T Consensus 329 ~l~~~~a~~~l~~~G~~Gl~~~a~~~~~~a~~l~~~L~ 366 (481)
T PRK04366 329 FGVLVRAYAYIRSLGAEGLREVSEDAVLNANYLKARLK 366 (481)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 4778899999999994 67887777777888887654
No 29
>COG0811 TolQ Biopolymer transport proteins [Intracellular trafficking and secretion]
Probab=24.61 E-value=1.5e+02 Score=20.78 Aligned_cols=37 Identities=16% Similarity=0.088 Sum_probs=29.3
Q ss_pred hhHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHHHH
Q psy11983 2 GCALLTLITWAYIRYSGEMTDIGIKIDDVANTVWDNR 38 (66)
Q Consensus 2 gl~L~~L~~WaYiRYSG~~revG~~ID~~A~~lwe~~ 38 (66)
|++.---++.+|-++++...+.-..+|+.++.+=+.+
T Consensus 173 GL~vAIPAvi~yn~l~r~~~~~~~~~e~~~~~l~~~~ 209 (216)
T COG0811 173 GLFVAIPAVVAYNVLRRKVEELLAKLEDFAEELELIL 209 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444455788999999999999999999999865543
No 30
>PF03589 Antiterm: Antitermination protein; InterPro: IPR003222 This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. The modified RNAP transcribes through termination sites that otherwise prevent expression of the regulated genes [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.91 E-value=1.9e+02 Score=18.18 Aligned_cols=35 Identities=6% Similarity=0.119 Sum_probs=28.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q psy11983 20 MTDIGIKIDDVANTVWDNRLVKLNQDFKEVTVRGQ 54 (66)
Q Consensus 20 ~revG~~ID~~A~~lwe~~l~p~~~~~~~~~~~~~ 54 (66)
++.|....+++++..|..-++|.|+.++..-..+-
T Consensus 52 ~~al~~~a~~~~~~~w~rk~k~~~~~lv~~~~aee 86 (95)
T PF03589_consen 52 IEALTQYAPKLAPRTWLRKWKPFYEALVMKCLAEE 86 (95)
T ss_pred HHHHHHHHHHHCHHHHHHHhhhHHHHHHHHHHHHH
Confidence 56788889999999999999999998875554443
No 31
>PF10823 DUF2568: Protein of unknown function (DUF2568); InterPro: IPR021214 One member in this family is annotated as yrdB which is part of a four gene operon however currently no function is known.
Probab=22.26 E-value=1.8e+02 Score=18.38 Aligned_cols=44 Identities=16% Similarity=0.075 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHhhccchhhH-HHHHHHHHHHHHHHHHHHHHHHH
Q psy11983 3 CALLTLITWAYIRYSGEMTDI-GIKIDDVANTVWDNRLVKLNQDF 46 (66)
Q Consensus 3 l~L~~L~~WaYiRYSG~~rev-G~~ID~~A~~lwe~~l~p~~~~~ 46 (66)
.++.++..|+|...++-.|-+ |..+.-++-.+|-.++.|-...-
T Consensus 10 a~l~~l~~wG~~~~~~~~~~~l~i~~p~~~a~~Wg~f~APka~~r 54 (93)
T PF10823_consen 10 AALAALGYWGFRLGGWWWKILLAIGLPLLAAVLWGLFGAPKAPRR 54 (93)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHcCCCCccc
Confidence 367889999999885555543 44567889999999887764443
No 32
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=21.53 E-value=68 Score=17.97 Aligned_cols=10 Identities=30% Similarity=0.491 Sum_probs=7.3
Q ss_pred hhccchhhHH
Q psy11983 15 RYSGEMTDIG 24 (66)
Q Consensus 15 RYSG~~revG 24 (66)
=-||||.+.-
T Consensus 25 vk~GQfdD~e 34 (45)
T PF03597_consen 25 VKSGQFDDLE 34 (45)
T ss_pred HccCCCCCCc
Confidence 4589998753
No 33
>PF15182 OTOS: Otospiralin
Probab=20.97 E-value=1.2e+02 Score=18.92 Aligned_cols=24 Identities=33% Similarity=0.880 Sum_probs=16.8
Q ss_pred HHHHHhhccchhhHHH--HHHHHHHHHHH
Q psy11983 10 TWAYIRYSGEMTDIGI--KIDDVANTVWD 36 (66)
Q Consensus 10 ~WaYiRYSG~~revG~--~ID~~A~~lwe 36 (66)
.|.|+-| ||.+|. .|.++|.+..-
T Consensus 27 FW~Yvey---FrtlGAY~~indmARtfFA 52 (69)
T PF15182_consen 27 FWNYVEY---FRTLGAYNQINDMARTFFA 52 (69)
T ss_pred HHHHHHH---HHHhccHHHHHHHHHHHHh
Confidence 5888865 888886 46777766543
No 34
>KOG1782|consensus
Probab=20.68 E-value=76 Score=21.89 Aligned_cols=19 Identities=21% Similarity=0.258 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy11983 25 IKIDDVANTVWDNRLVKLN 43 (66)
Q Consensus 25 ~~ID~~A~~lwe~~l~p~~ 43 (66)
..+||.|+.+.+.+.+.++
T Consensus 37 RSfDQFaNlvL~~~iERi~ 55 (129)
T KOG1782|consen 37 RSFDQFANLVLQGVIERIF 55 (129)
T ss_pred hhHHHHHHHHHHhhhhhee
Confidence 4689999999998876655
No 35
>PHA00450 host dGTPase inhibitor
Probab=20.46 E-value=76 Score=20.50 Aligned_cols=17 Identities=18% Similarity=0.362 Sum_probs=14.2
Q ss_pred hccchhhHHHHHHHHHH
Q psy11983 16 YSGEMTDIGIKIDDVAN 32 (66)
Q Consensus 16 YSG~~revG~~ID~~A~ 32 (66)
|||++-++-.++|.+=+
T Consensus 5 YSGNL~afKaA~~RL~q 21 (85)
T PHA00450 5 YSGNLNAFKAATARLFE 21 (85)
T ss_pred ccCcHHHHHHHHHHHHh
Confidence 89999999888887654
Done!