Query 000632
Match_columns 1381
No_of_seqs 86 out of 101
Neff 3.4
Searched_HMMs 46136
Date Mon Apr 1 21:06:45 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000632hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1886 BAH domain proteins [T 99.5 2.7E-15 5.9E-20 173.3 5.2 251 1-259 192-462 (464)
2 smart00509 TFS2N Domain in the 99.1 6.3E-11 1.4E-15 108.8 4.9 56 148-203 18-75 (75)
3 cd00183 TFIIS_I N-terminal dom 99.1 1.5E-10 3.2E-15 106.2 6.3 56 147-202 19-76 (76)
4 PF08711 Med26: TFIIS helical 98.9 1E-09 2.2E-14 93.9 3.8 50 153-202 1-53 (53)
5 TIGR01385 TFSII transcription 98.8 6.2E-09 1.4E-13 116.9 5.2 58 148-205 20-79 (299)
6 KOG1105 Transcription elongati 98.4 1.4E-07 3E-12 105.9 4.6 64 149-212 23-90 (296)
7 PLN02976 amine oxidase 97.1 0.00088 1.9E-08 88.2 7.6 102 91-205 1256-1360(1713)
8 KOG1793 Uncharacterized conser 95.1 0.03 6.5E-07 65.9 5.8 120 71-201 159-290 (417)
9 PF11467 LEDGF: Lens epitheliu 89.2 0.51 1.1E-05 47.4 4.5 55 148-202 22-80 (106)
10 COG5139 Uncharacterized conser 79.9 3.1 6.6E-05 48.3 5.7 51 152-202 233-287 (397)
11 KOG2821 RNA polymerase II tran 71.5 1.3 2.9E-05 53.3 0.1 54 149-204 25-80 (433)
12 PHA02763 hypothetical protein; 52.6 10 0.00022 37.6 2.2 43 89-131 36-79 (102)
13 PF06371 Drf_GBD: Diaphanous G 44.8 49 0.0011 34.4 6.0 92 98-194 88-182 (187)
14 PF04818 CTD_bind: RNA polymer 40.0 20 0.00044 32.1 2.1 57 116-200 2-60 (64)
15 KOG3753 Circadian clock protei 32.4 1.7E+02 0.0037 39.1 8.9 12 1265-1276 864-875 (1114)
16 KOG0166 Karyopherin (importin) 30.6 60 0.0013 40.8 4.6 111 67-198 360-485 (514)
17 PF05589 DUF768: Protein of un 28.3 66 0.0014 30.4 3.4 49 116-170 3-51 (64)
18 KOG4464 Signaling protein RIC- 25.7 1.2E+02 0.0026 37.6 5.7 58 73-131 141-201 (532)
19 cd03569 VHS_Hrs_Vps27p VHS dom 24.3 6.7E+02 0.015 26.4 10.2 109 54-204 5-119 (142)
20 cd00020 ARM Armadillo/beta-cat 24.2 3.6E+02 0.0078 25.0 7.6 106 72-195 8-116 (120)
21 PF14726 RTTN_N: Rotatin, an a 20.3 98 0.0021 31.1 3.1 50 146-195 45-96 (98)
22 cd03561 VHS VHS domain family; 20.1 8.6E+02 0.019 25.0 9.9 24 181-204 94-117 (133)
No 1
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.55 E-value=2.7e-15 Score=173.28 Aligned_cols=251 Identities=17% Similarity=0.020 Sum_probs=208.8
Q ss_pred CcccccCCCCCCCCCCCCCccccCCCCCcccccc--------cCCCCcCcC----CCCCCcchhh------HHHHHhhhh
Q 000632 1 MHATMQQGGRSPKPLNGPTSTSQLKPSSDSVQNS--------VSSFPSQVK----DSGHGRSENV------LRSEISKIT 62 (1381)
Q Consensus 1 Mha~vQ~GGrSPk~lngptstq~lK~gsd~~qn~--------~sSf~sq~K----~sg~~r~~~~------lk~ei~~Lt 62 (1381)
||...++..+...+++.+.-+|| |..+++.--+ -.+|---.+ +-......+. .-+++.+-+
T Consensus 192 ~~~~~~p~~~~t~~~~~~~~~~~-~s~~~~~~r~ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~ 270 (464)
T KOG1886|consen 192 RGTLPDPKKVQTLNAAASKRSQQ-KSEISSLSRASSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAG 270 (464)
T ss_pred CCCCCCccccccccccccceecc-ccccccccccccccccccccCCCCCCCcccccccccccchhhccccccccccCCCc
Confidence 56778889999999888888887 5444411100 011111111 1111122222 234566677
Q ss_pred ccCCccChhhHHHHHHHhccCcccccccccchhHHHHHHHhccchhhhhhhhhccChhhHHHHHHHHhccccCCCCCCCC
Q 000632 63 ENGGLVDFEGVEKFIQLMVPDRNERKIDLVCRSMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKD 142 (1381)
Q Consensus 63 ekgGL~~~e~V~kLV~LM~~~~~~kk~~l~~R~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~sp~~ 142 (1381)
++|++..++.|..++.||+..-++.+.|+..+..++-+|..+=..+||-.|.+++|..+.++|+|+.|.+++.++..++.
T Consensus 271 ~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~~~~ 350 (464)
T KOG1886|consen 271 DQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPDGQSSPS 350 (464)
T ss_pred ccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCCCccCcc
Confidence 88999999999999999999999988999999999999999999999999999999999999999999999999999999
Q ss_pred CCchhhhhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHHHHHHHHhhhhhhhccCCCCccccCCCC
Q 000632 143 GDKAIEEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWKKRVEAEMNAKSGSNQAVSGLAR 220 (1381)
Q Consensus 143 ~dk~vee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~LvdsWKk~V~aE~daKsgs~q~vsW~~k 220 (1381)
.++-+.++.+.|+.+|++++++++.+.-+++ -+++|+-|..+||-..++++++.|+.++..+|++|++++|.+.|+.|
T Consensus 351 ~~~~~~d~~~~l~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~~~~~~~~~~q~~~~~~k 430 (464)
T KOG1886|consen 351 SMKLNDDDYDGLCVGLELTAGSLYLYCGQEGLICAGHLPCPMLPEVKLSPVAAVHREGLLLAPSSVPKGTPFQHPPWPEK 430 (464)
T ss_pred ccccCchhHHHHHHhhhhhccchhhhcccccceeccccCCCCCCCcCcccccccchhhhcccceeccCCCCccCCCChhh
Confidence 9999999999999999999999999999988 99999999999999999999999999999999999999999999999
Q ss_pred CCCCccccCCCCCCCCCcchhhccccccccccccccccc
Q 000632 221 PRIPEVSHGGNRNSGSSSEIAIKSSSMQLSTSKTASVKL 259 (1381)
Q Consensus 221 ~~~~Evsh~gnr~sg~sse~~~KSsv~q~s~SK~~svK~ 259 (1381)
-.|++ |++|++.| +++.....+.+.+.+++|.
T Consensus 431 -----~~~~~-ret~~~~e-a~~~~~~~~~a~~~~~~k~ 462 (464)
T KOG1886|consen 431 -----RLCSP-RETGVNGE-AICGVLPLLVAHAGTTCKG 462 (464)
T ss_pred -----cccCc-cccCCchh-cccCCchhhhhcccccccC
Confidence 56755 99999999 6666556676777776664
No 2
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.11 E-value=6.3e-11 Score=108.80 Aligned_cols=56 Identities=41% Similarity=0.555 Sum_probs=53.8
Q ss_pred hhhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHHHHHHHHhhhh
Q 000632 148 EEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWKKRVEA 203 (1381)
Q Consensus 148 ee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~LvdsWKk~V~a 203 (1381)
++.++++|++|+.+||+.++|++|+| .||.||+|+|++|+++|+.||+.||+.|++
T Consensus 18 ~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~~ 75 (75)
T smart00509 18 VSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75 (75)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhcC
Confidence 67899999999999999999999999 999999999999999999999999999863
No 3
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.09 E-value=1.5e-10 Score=106.19 Aligned_cols=56 Identities=39% Similarity=0.548 Sum_probs=53.5
Q ss_pred hhhhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHHHHHHHHhhh
Q 000632 147 IEEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWKKRVE 202 (1381)
Q Consensus 147 vee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~LvdsWKk~V~ 202 (1381)
-++.++++|++|+++||+.++|++|+| .||.||+|.+++|+++|+.||+.||+.|+
T Consensus 19 ~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 19 EVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred CHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 367899999999999999999999999 99999999999999999999999999874
No 4
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=98.90 E-value=1e-09 Score=93.93 Aligned_cols=50 Identities=40% Similarity=0.701 Sum_probs=45.7
Q ss_pred HHHHHhhcCCcchhhhhhcCc--cccccccC-CCHHHHHHHHHHHHHHHHhhh
Q 000632 153 VSLRALDKLPVNLHALQMGNM--FVNHLRTH-KNLEIQKKARSLVDTWKKRVE 202 (1381)
Q Consensus 153 ~LLrAL~kLPIdle~Lkst~I--tVn~LRkh-kn~EVqk~Ak~LvdsWKk~V~ 202 (1381)
++|+.|++|||+.+.|++|+| .|+.|++| .+++|+++|+.||+.||+.|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 589999999999999999999 99999999 999999999999999999985
No 5
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=98.76 E-value=6.2e-09 Score=116.95 Aligned_cols=58 Identities=34% Similarity=0.465 Sum_probs=55.6
Q ss_pred hhhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHHHHHHHHhhhhhh
Q 000632 148 EEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWKKRVEAEM 205 (1381)
Q Consensus 148 ee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~LvdsWKk~V~aE~ 205 (1381)
++.+|+||+.|++++|++++|++|.| .||+||+|.+.+|+++|+.||+.||+.|..+.
T Consensus 20 ~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~k 79 (299)
T TIGR01385 20 VEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKNK 79 (299)
T ss_pred HHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhhc
Confidence 45899999999999999999999999 99999999999999999999999999999873
No 6
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=98.44 E-value=1.4e-07 Score=105.89 Aligned_cols=64 Identities=42% Similarity=0.574 Sum_probs=56.0
Q ss_pred hhHHHHHHHhhcCCcchhhhhhcCc--ccc-ccccCCCHHHHHHHHHHHHHHHHhhhhh-hhccCCCC
Q 000632 149 EFPLVSLRALDKLPVNLHALQMGNM--FVN-HLRTHKNLEIQKKARSLVDTWKKRVEAE-MNAKSGSN 212 (1381)
Q Consensus 149 e~ll~LLrAL~kLPIdle~Lkst~I--tVn-~LRkhkn~EVqk~Ak~LvdsWKk~V~aE-~daKsgs~ 212 (1381)
+.+|++|..|+++||++++|+.|+| .|| .|++|+|+||.++||.||+.||++|+.. -..|++-+
T Consensus 23 ~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~~~~~k~~~~ 90 (296)
T KOG1105|consen 23 EAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKSPGREKSGDN 90 (296)
T ss_pred HHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcccccccCccc
Confidence 6899999999999999999999999 999 5557999999999999999999999985 34444433
No 7
>PLN02976 amine oxidase
Probab=97.09 E-value=0.00088 Score=88.17 Aligned_cols=102 Identities=22% Similarity=0.258 Sum_probs=86.7
Q ss_pred ccchhHHHHHHHhccchhhhhhhhhccChhhHHHHHHHHhccccCCCCCCCCCCchhhhhHHHHHHHhhcCCcchhhhhh
Q 000632 91 LVCRSMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQM 170 (1381)
Q Consensus 91 l~~R~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~sp~~~dk~vee~ll~LLrAL~kLPIdle~Lks 170 (1381)
.++|-.|++.|..--..+.-++.++-.||.+||.||-+.. ||-|. +++.-+|+-|--+|.||-+|..
T Consensus 1256 ~~gr~~~~~~~~~~~~~~~~~~a~~~~gl~~l~~w~~~~~-~~~~~------------~l~~~~~~ll~~~~~d~~a~r~ 1322 (1713)
T PLN02976 1256 TAGRLHLAKELLNLPVETLKSFAGTKEGLATLNSWILDSM-GKDGT------------QLLRHCVRLLVLVSTDLLAVRL 1322 (1713)
T ss_pred cccHHHHHHHHHhCCHHHHHHHhcccchHHHHHHHHHHHh-cccHH------------HHHHHHHHHHhhcchhHHHHHh
Confidence 5578777777755555566677788999999999999994 56653 5888899999999999999999
Q ss_pred cCc--cccccc-cCCCHHHHHHHHHHHHHHHHhhhhhh
Q 000632 171 GNM--FVNHLR-THKNLEIQKKARSLVDTWKKRVEAEM 205 (1381)
Q Consensus 171 t~I--tVn~LR-khkn~EVqk~Ak~LvdsWKk~V~aE~ 205 (1381)
+|| ||++=- -|.+.+|+..|+.|++.|...+..|.
T Consensus 1323 sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~ 1360 (1713)
T PLN02976 1323 SGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREK 1360 (1713)
T ss_pred ccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhh
Confidence 999 777654 69999999999999999999999998
No 8
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.14 E-value=0.03 Score=65.93 Aligned_cols=120 Identities=22% Similarity=0.393 Sum_probs=81.1
Q ss_pred hhHHHHHHHhccCccc-ccccccc-----h-hHHHHHHHhccchhhhhhhhhccChhhHHHHHHHHhccccCCCCCCCCC
Q 000632 71 EGVEKFIQLMVPDRNE-RKIDLVC-----R-SMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDG 143 (1381)
Q Consensus 71 e~V~kLV~LM~~~~~~-kk~~l~~-----R-~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~sp~~~ 143 (1381)
.-|..|++.|+..-.. ..+..-+ . -+|--|.+--.++.+-+.|+--+=|-.|..||.=.-.|.+ |.
T Consensus 159 ~~v~~l~~~m~~aa~~D~~~N~e~kPA~~Klk~Lp~v~~vL~k~~L~et~LDngvL~~lk~WLePLPD~SL-----Pa-- 231 (417)
T KOG1793|consen 159 DEVSRLMERMEDAAEKDRELNREGKPATQKLKLLPLVVAVLSKKALQETFLDNGVLDSLKEWLEPLPDGSL-----PA-- 231 (417)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccCchHHHHhccHHHHHHHhhhhHHHHHHhhhHHHHHHHHhccCCCCCC-----cc--
Confidence 5677888888743322 0000111 1 1222223333567778889999999999999987776544 31
Q ss_pred CchhhhhHHHHHHHhhcCCcch-hhhhhcCc--cccccccCCCH--HHHHHHHHHHHHHHHhh
Q 000632 144 DKAIEEFPLVSLRALDKLPVNL-HALQMGNM--FVNHLRTHKNL--EIQKKARSLVDTWKKRV 201 (1381)
Q Consensus 144 dk~vee~ll~LLrAL~kLPIdl-e~Lkst~I--tVn~LRkhkn~--EVqk~Ak~LvdsWKk~V 201 (1381)
-+-=-.||+.|..|||++ |+|+.+|| -|=-|-+|+.+ +++..|..||..|-.-|
T Consensus 232 ----l~Ir~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI 290 (417)
T KOG1793|consen 232 ----LNIRKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPI 290 (417)
T ss_pred ----hHHHHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccc
Confidence 233457888999999999 99999999 55555566554 58888999999997644
No 9
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=89.17 E-value=0.51 Score=47.36 Aligned_cols=55 Identities=29% Similarity=0.273 Sum_probs=46.4
Q ss_pred hhhHHHHHHHhhcCCcchhhhhhcCc---ccccccc-CCCHHHHHHHHHHHHHHHHhhh
Q 000632 148 EEFPLVSLRALDKLPVNLHALQMGNM---FVNHLRT-HKNLEIQKKARSLVDTWKKRVE 202 (1381)
Q Consensus 148 ee~ll~LLrAL~kLPIdle~Lkst~I---tVn~LRk-hkn~EVqk~Ak~LvdsWKk~V~ 202 (1381)
-+-+|.+|..|..|||+...|+++-- |+.+||+ ..|..|+++|-.|+++.|..+-
T Consensus 22 v~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 22 VKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence 35799999999999999999999766 9999998 6788999999999999999995
No 10
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=79.85 E-value=3.1 Score=48.32 Aligned_cols=51 Identities=20% Similarity=0.412 Sum_probs=41.5
Q ss_pred HHHHHHhhcCCcchhhhhhcCc-ccc---ccccCCCHHHHHHHHHHHHHHHHhhh
Q 000632 152 LVSLRALDKLPVNLHALQMGNM-FVN---HLRTHKNLEIQKKARSLVDTWKKRVE 202 (1381)
Q Consensus 152 l~LLrAL~kLPIdle~Lkst~I-tVn---~LRkhkn~EVqk~Ak~LvdsWKk~V~ 202 (1381)
-.||.+|.+|||--|+|..+|| .|- -+.+....+|+..|+.||-.|-.-|-
T Consensus 233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIi 287 (397)
T COG5139 233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPII 287 (397)
T ss_pred HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhcccc
Confidence 4577888899999999999999 332 33467888999999999999976553
No 11
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=71.46 E-value=1.3 Score=53.34 Aligned_cols=54 Identities=28% Similarity=0.321 Sum_probs=49.0
Q ss_pred hhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHHHHHHHHhhhhh
Q 000632 149 EFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWKKRVEAE 204 (1381)
Q Consensus 149 e~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~LvdsWKk~V~aE 204 (1381)
.-++.-|.-|-.||+.+++|..++| +|+.||+|. ++-..|+.|+-.||+.|-.+
T Consensus 25 kR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d 80 (433)
T KOG2821|consen 25 KRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVD 80 (433)
T ss_pred HHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcccc
Confidence 4678888889999999999999999 999999998 78999999999999999744
No 12
>PHA02763 hypothetical protein; Provisional
Probab=52.61 E-value=10 Score=37.61 Aligned_cols=43 Identities=30% Similarity=0.560 Sum_probs=33.6
Q ss_pred ccccchhHHHHHHH-hccchhhhhhhhhccChhhHHHHHHHHhc
Q 000632 89 IDLVCRSMLAGVVA-AADKFDCLSKFVQVKGLHVFDEWLQEVHK 131 (1381)
Q Consensus 89 ~~l~~R~~la~vIa-aTes~DcL~~FVql~GL~vLd~WLqea~k 131 (1381)
+.+..|--.+.||| |--..|||..+||..|.--+++||.+|+.
T Consensus 36 l~v~dr~f~gKvIa~ap~t~~~LsKYv~~SGFe~VEeWl~eArr 79 (102)
T PHA02763 36 LKVGDKRFPGKVIAKAPVTEYCLSKYVKFSGFENVEEWLNEARR 79 (102)
T ss_pred EEecCccccceEEEecCchHHHHHHHhhhcchhhHHHHHHHHHH
Confidence 44455555666664 23357999999999999999999999987
No 13
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=44.84 E-value=49 Score=34.38 Aligned_cols=92 Identities=23% Similarity=0.240 Sum_probs=64.9
Q ss_pred HHHHHhccchhhhhhhhhccChhhHHHHHHHHhccccCCCCCCCCCCchhhhhHHHHHHHhhcCCcchhhhhhcCccccc
Q 000632 98 AGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQMGNMFVNH 177 (1381)
Q Consensus 98 a~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~sp~~~dk~vee~ll~LLrAL~kLPIdle~Lkst~ItVn~ 177 (1381)
+.|-..|..-+=++.|+..+|+.+|-++|...+.-..- .+.|..++..++.-||+|-+-..-++.+..+.-.|+.
T Consensus 88 L~v~Lrt~~~~Wv~~Fl~~~G~~~L~~~L~~~~~~~~~-----~~~~~~~~~~~l~Clkal~n~~~G~~~v~~~~~~v~~ 162 (187)
T PF06371_consen 88 LRVSLRTNPISWVQEFLELGGLEALLNVLSKLNKKKEK-----SEEDIDIEHECLRCLKALMNTKYGLEAVLSHPDSVNL 162 (187)
T ss_dssp HHHHHHHS-HHHHHHH-HHHHHHHHHHHHHHHHTHHCT-----CTTCHHHHHHHHHHHHHHTSSHHHHHHHHCSSSHHHH
T ss_pred HHHHhccCCchHHHHhccCCCHHHHHHHHHHhhhhhhh-----cchhHHHHHHHHHHHHHHHccHHHHHHHHcCcHHHHH
Confidence 34555778888899999999999999999999883221 2466677778888888888888777777774443333
Q ss_pred c---ccCCCHHHHHHHHHHH
Q 000632 178 L---RTHKNLEIQKKARSLV 194 (1381)
Q Consensus 178 L---Rkhkn~EVqk~Ak~Lv 194 (1381)
| ....+..+++.|-.|.
T Consensus 163 i~~~L~s~~~~~r~~~leiL 182 (187)
T PF06371_consen 163 IALSLDSPNIKTRKLALEIL 182 (187)
T ss_dssp HHHT--TTSHHHHHHHHHHH
T ss_pred HHHHHCCCCHHHHHHHHHHH
Confidence 3 3477778887776654
No 14
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=39.98 E-value=20 Score=32.11 Aligned_cols=57 Identities=23% Similarity=0.402 Sum_probs=37.1
Q ss_pred ccChhhHHHHHHHHhccccCCCCCCCCCCchhhhhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHH
Q 000632 116 VKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSL 193 (1381)
Q Consensus 116 l~GL~vLd~WLqea~kGk~g~~~sp~~~dk~vee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~L 193 (1381)
|..|-|+|+.||.+++ | ..|..++.+- ..| .+.++.+..+++++++...|
T Consensus 2 L~~lYl~ndI~q~sk~-k--------~~~~f~~~F~-------------------~~l~~~~~~~~~~~~~~~~~kv~rl 53 (64)
T PF04818_consen 2 LALLYLANDILQNSKR-K--------NPDEFAPAFS-------------------PVLPDAFAHAYKNVDPEVRKKVQRL 53 (64)
T ss_dssp HHHHHHHHHHHHHHHH-H--------TTHCHHHHHH-------------------CCHHHHHHHHCCCS-HHHHHHHHHH
T ss_pred cceeehHHHHHHHhhh-c--------ChHHHHHHHH-------------------HHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 4567899999999987 2 1112221111 122 34456666699999999999
Q ss_pred HHHHHHh
Q 000632 194 VDTWKKR 200 (1381)
Q Consensus 194 vdsWKk~ 200 (1381)
++-|+++
T Consensus 54 l~iW~~r 60 (64)
T PF04818_consen 54 LNIWEER 60 (64)
T ss_dssp HHHHHHC
T ss_pred HHHhhCC
Confidence 9999864
No 15
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=32.40 E-value=1.7e+02 Score=39.05 Aligned_cols=12 Identities=25% Similarity=0.279 Sum_probs=7.0
Q ss_pred CCccccCCCCcc
Q 000632 1265 GRLCFPAVNSQL 1276 (1381)
Q Consensus 1265 g~~cfp~v~sQ~ 1276 (1381)
..+-||.+.++.
T Consensus 864 s~~~fPs~~~p~ 875 (1114)
T KOG3753|consen 864 SAPLFPSYYSPA 875 (1114)
T ss_pred cCCCCCcccCCC
Confidence 344677666654
No 16
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.59 E-value=60 Score=40.77 Aligned_cols=111 Identities=20% Similarity=0.228 Sum_probs=68.1
Q ss_pred ccChhhHHHHHHHhccCccc-ccccccchhHHHHHHHhccchhhhhhhhhccChhhHHHHHHHHhccccCCCCCCCCCCc
Q 000632 67 LVDFEGVEKFIQLMVPDRNE-RKIDLVCRSMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDGDK 145 (1381)
Q Consensus 67 L~~~e~V~kLV~LM~~~~~~-kk~~l~~R~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~sp~~~dk 145 (1381)
+++..-++.|+++|+..... || .-+-...-+.+.-+++-+...|..+=++=|=.-| . .-|.
T Consensus 360 Vida~l~p~Li~~l~~~ef~~rK----EAawaIsN~ts~g~~~qi~yLv~~giI~plcdlL----~----------~~D~ 421 (514)
T KOG0166|consen 360 VIDANLIPVLINLLQTAEFDIRK----EAAWAISNLTSSGTPEQIKYLVEQGIIKPLCDLL----T----------CPDV 421 (514)
T ss_pred HHHcccHHHHHHHHhccchHHHH----HHHHHHHhhcccCCHHHHHHHHHcCCchhhhhcc----c----------CCCh
Confidence 45666778999999976643 33 2244444455666688888888877444444434 1 1122
Q ss_pred hhhhhHHHHHHHhhcCCcch------------hhhhhcCc--cccccccCCCHHHHHHHHHHHHHHH
Q 000632 146 AIEEFPLVSLRALDKLPVNL------------HALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWK 198 (1381)
Q Consensus 146 ~vee~ll~LLrAL~kLPIdl------------e~Lkst~I--tVn~LRkhkn~EVqk~Ak~LvdsWK 198 (1381)
. .+...|.+|+.|=--- ..+..++. ++..|..|+|++|.++|-.||++.=
T Consensus 422 ~---ii~v~Ld~l~nil~~~e~~~~~~~n~~~~~IEe~ggldkiE~LQ~hen~~Iy~~A~~II~~yf 485 (514)
T KOG0166|consen 422 K---IILVALDGLENILKVGEAEKNRGTNPLAIMIEEAGGLDKIENLQSHENEEIYKKAYKIIDTYF 485 (514)
T ss_pred H---HHHHHHHHHHHHHHHHHHhccccccHHHHHHHHccChhHHHHhhccccHHHHHHHHHHHHHhc
Confidence 2 2444444443321111 22334555 9999999999999999999999753
No 17
>PF05589 DUF768: Protein of unknown function (DUF768); InterPro: IPR008486 This family consists of several uncharacterised hypothetical proteins from Rhizobium loti (Mesorhizobium loti).
Probab=28.29 E-value=66 Score=30.38 Aligned_cols=49 Identities=12% Similarity=0.251 Sum_probs=37.6
Q ss_pred ccChhhHHHHHHHHhccccCCCCCCCCCCchhhhhHHHHHHHhhcCCcchhhhhh
Q 000632 116 VKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQM 170 (1381)
Q Consensus 116 l~GL~vLd~WLqea~kGk~g~~~sp~~~dk~vee~ll~LLrAL~kLPIdle~Lks 170 (1381)
-+|+.||+.|+.+-.- +.-.++ -.++.++..+|+.+-+++-|..+-+..
T Consensus 3 ~r~~~Fl~~WI~e~V~----~~~~~d--~is~~~La~kl~adA~a~Gi~~~ei~e 51 (64)
T PF05589_consen 3 TRGIEFLDSWIAENVP----DTPKAD--IISAAELAEKLFADAEAAGIPREEIEE 51 (64)
T ss_pred chHHHHHHHHHHhcCC----Cccccc--hhhHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 3689999999998654 332222 357799999999999999998887654
No 18
>KOG4464 consensus Signaling protein RIC-8/synembryn (regulates neurotransmitter secretion) [Signal transduction mechanisms]
Probab=25.72 E-value=1.2e+02 Score=37.63 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=34.2
Q ss_pred HHHHHHHhccCcccccccccch--hHHHHHHHhccchhhhhhhhh-ccChhhHHHHHHHHhc
Q 000632 73 VEKFIQLMVPDRNERKIDLVCR--SMLAGVVAAADKFDCLSKFVQ-VKGLHVFDEWLQEVHK 131 (1381)
Q Consensus 73 V~kLV~LM~~~~~~kk~~l~~R--~~la~vIaaTes~DcL~~FVq-l~GL~vLd~WLqea~k 131 (1381)
+.||.++...+...+...++.. ..|+..|.|-+ .|.-.+|++ +.|+.++-.||.+...
T Consensus 141 ~~~ll~~v~~~~er~~~~~~~~~dlrLLflltale-~~~Rsql~~~l~Gl~~lt~~led~lg 201 (532)
T KOG4464|consen 141 TGKLLQRVLGEFERNFPKDSSIFDLRLLFLLTALE-TDHRSQLIAELLGLELLTNWLEDKLG 201 (532)
T ss_pred HHHHHHHHHHHHHhcCCccchhhHHHHHHHHHHhh-HHHHHHHHHHhcccHHHHHHhhcccc
Confidence 3445555554443322222222 44555555555 366555554 9999999999998766
No 19
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=24.29 E-value=6.7e+02 Score=26.45 Aligned_cols=109 Identities=19% Similarity=0.229 Sum_probs=63.2
Q ss_pred HHHHHhhhhc-cCCccChhhHHHHHHHhccCcccccccccchhHHHHHHH-----hccchhhhhhhhhccChhhHHHHHH
Q 000632 54 LRSEISKITE-NGGLVDFEGVEKFIQLMVPDRNERKIDLVCRSMLAGVVA-----AADKFDCLSKFVQVKGLHVFDEWLQ 127 (1381)
Q Consensus 54 lk~ei~~Lte-kgGL~~~e~V~kLV~LM~~~~~~kk~~l~~R~~la~vIa-----aTes~DcL~~FVql~GL~vLd~WLq 127 (1381)
+...|.+.|. .-.-.+|+.+-+|..+...+.+. ...+-|++-=.+-. +-..-..|+.+|+=-|.+|..+.-.
T Consensus 5 ~~~~I~kATs~~l~~~dw~~ileicD~In~~~~~--~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas 82 (142)
T cd03569 5 FDELIEKATSELLGEPDLASILEICDMIRSKDVQ--PKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVAS 82 (142)
T ss_pred HHHHHHHHcCcccCccCHHHHHHHHHHHhCCCCC--HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhh
Confidence 5566777777 66778888888888888766443 11333322211110 0011245566666556666544331
Q ss_pred HHhccccCCCCCCCCCCchhhhhHHHHHHHhhcCCcchhhhhhcCccccccccCCCHHHHHHHHHHHHHHHHhhhhh
Q 000632 128 EVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQMGNMFVNHLRTHKNLEIQKKARSLVDTWKKRVEAE 204 (1381)
Q Consensus 128 ea~kGk~g~~~sp~~~dk~vee~ll~LLrAL~kLPIdle~Lkst~ItVn~LRkhkn~EVqk~Ak~LvdsWKk~V~aE 204 (1381)
+ +|+-+|.+-+. ...+.+|++++..||..|...+..+
T Consensus 83 ---~-----------------~fl~~l~~l~~--------------------~~~~~~Vk~kil~li~~W~~~f~~~ 119 (142)
T cd03569 83 ---R-----------------EFMDELKDLIK--------------------TTKNEEVRQKILELIQAWALAFRNK 119 (142)
T ss_pred ---H-----------------HHHHHHHHHHc--------------------ccCCHHHHHHHHHHHHHHHHHhCCC
Confidence 1 23333333211 1467889999999999999887643
No 20
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=24.16 E-value=3.6e+02 Score=25.03 Aligned_cols=106 Identities=21% Similarity=0.261 Sum_probs=61.7
Q ss_pred hHHHHHHHhccCcccccccccchhHHHHHHHhccchhhhhhhhhccChhhHHHHHHHHhccccCCCCCCCCCCchhhhhH
Q 000632 72 GVEKFIQLMVPDRNERKIDLVCRSMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIEEFP 151 (1381)
Q Consensus 72 ~V~kLV~LM~~~~~~kk~~l~~R~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~sp~~~dk~vee~l 151 (1381)
.++.|+.+|+..... +....-..|.+ | +....++...|++.++++.|-.=|.+ .|..+-..+
T Consensus 8 ~i~~l~~~l~~~~~~--~~~~a~~~l~~-l-~~~~~~~~~~~~~~~~i~~l~~~l~~--------------~~~~v~~~a 69 (120)
T cd00020 8 GLPALVSLLSSSDEN--VQREAAWALSN-L-SAGNNDNIQAVVEAGGLPALVQLLKS--------------EDEEVVKAA 69 (120)
T ss_pred ChHHHHHHHHcCCHH--HHHHHHHHHHH-H-hcCCHHHHHHHHHCCChHHHHHHHhC--------------CCHHHHHHH
Confidence 578899999855311 11111122222 2 22348899999999998888877754 133444556
Q ss_pred HHHHHHhhcCC-cchhhhhhcCc--cccccccCCCHHHHHHHHHHHH
Q 000632 152 LVSLRALDKLP-VNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVD 195 (1381)
Q Consensus 152 l~LLrAL~kLP-Idle~Lkst~I--tVn~LRkhkn~EVqk~Ak~Lvd 195 (1381)
+..|..|-.-+ -..+.+...++ .+-++-...+.+++..|-.++.
T Consensus 70 ~~~L~~l~~~~~~~~~~~~~~g~l~~l~~~l~~~~~~~~~~a~~~l~ 116 (120)
T cd00020 70 LWALRNLAAGPEDNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGALS 116 (120)
T ss_pred HHHHHHHccCcHHHHHHHHHCCChHHHHHHHhcCCHHHHHHHHHHHH
Confidence 66666554433 33444555555 4444444557888888776654
No 21
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=20.30 E-value=98 Score=31.14 Aligned_cols=50 Identities=24% Similarity=0.282 Sum_probs=44.4
Q ss_pred hhhhhHHHHHHHhhcCCcchhhhhhcCc--cccccccCCCHHHHHHHHHHHH
Q 000632 146 AIEEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVD 195 (1381)
Q Consensus 146 ~vee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkhkn~EVqk~Ak~Lvd 195 (1381)
+..+.+|+||+-|.+-|--..+|..-|. ..++||++-+...+...-.|++
T Consensus 45 ~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 45 PMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred ccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 5688999999999999999999999887 9999999999888888777665
No 22
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=20.13 E-value=8.6e+02 Score=24.99 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHHHHHhhhhh
Q 000632 181 HKNLEIQKKARSLVDTWKKRVEAE 204 (1381)
Q Consensus 181 hkn~EVqk~Ak~LvdsWKk~V~aE 204 (1381)
..+.+|++++..|+..|...+...
T Consensus 94 ~~~~~Vk~kil~ll~~W~~~f~~~ 117 (133)
T cd03561 94 KYDPKVREKALELILAWSESFGGH 117 (133)
T ss_pred CCCHHHHHHHHHHHHHHHHHhcCC
Confidence 357889999999999999877653
Done!