Query 001649
Match_columns 1038
No_of_seqs 79 out of 81
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:00:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001649hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00183 TFIIS_I N-terminal dom 99.2 6.9E-11 1.5E-15 105.5 7.4 57 95-151 20-76 (76)
2 smart00509 TFS2N Domain in the 99.1 6.9E-11 1.5E-15 105.6 5.3 57 95-151 18-74 (75)
3 PF08711 Med26: TFIIS helical 99.0 1.3E-10 2.7E-15 96.8 3.1 52 100-151 1-53 (53)
4 TIGR01385 TFSII transcription 98.5 5.3E-08 1.1E-12 107.0 4.6 59 95-153 20-78 (299)
5 KOG1105 Transcription elongati 98.1 4.4E-06 9.6E-11 91.9 5.5 58 96-153 23-81 (296)
6 PLN02976 amine oxidase 97.9 3.7E-05 8.1E-10 98.2 9.2 102 49-157 1261-1363(1713)
7 KOG1886 BAH domain proteins [T 97.3 8.3E-05 1.8E-09 85.9 1.3 138 13-154 272-415 (464)
8 KOG1793 Uncharacterized conser 96.9 0.0015 3.2E-08 74.5 6.2 134 20-160 159-301 (417)
9 COG5139 Uncharacterized conser 91.6 0.22 4.7E-06 55.9 4.6 76 79-154 211-291 (397)
10 cd00020 ARM Armadillo/beta-cat 82.3 11 0.00023 33.9 9.1 105 21-144 8-116 (120)
11 KOG2821 RNA polymerase II tran 77.0 0.92 2E-05 53.3 0.6 57 96-154 25-81 (433)
12 PHA02763 hypothetical protein; 65.5 7 0.00015 37.6 3.5 41 50-90 44-85 (102)
13 PF06371 Drf_GBD: Diaphanous G 60.2 39 0.00085 34.0 8.0 93 51-143 88-182 (187)
14 PF11467 LEDGF: Lens epitheliu 53.8 14 0.00031 36.3 3.5 55 97-151 24-80 (106)
15 KOG4368 Predicted RNA binding 43.1 79 0.0017 39.2 8.0 81 47-149 139-219 (757)
16 KOG0166 Karyopherin (importin) 42.9 84 0.0018 38.5 8.2 112 21-150 365-488 (514)
17 PF04818 CTD_bind: RNA polymer 42.3 44 0.00095 29.0 4.4 59 69-149 2-60 (64)
18 cd00176 SPEC Spectrin repeats, 40.7 1.8E+02 0.0039 28.6 9.0 112 39-150 80-199 (213)
19 PF12348 CLASP_N: CLASP N term 37.8 2E+02 0.0043 30.0 9.2 87 60-149 115-207 (228)
20 PF11698 V-ATPase_H_C: V-ATPas 36.8 95 0.002 31.3 6.3 41 107-147 74-114 (119)
21 PF03224 V-ATPase_H_N: V-ATPas 34.5 3.3E+02 0.0071 30.5 10.8 91 47-144 216-310 (312)
22 PF02084 Bindin: Bindin; Inte 32.8 19 0.00041 39.7 0.9 42 89-132 100-142 (238)
23 PLN03200 cellulose synthase-in 27.6 1.6E+02 0.0034 41.8 7.9 132 2-145 717-857 (2102)
24 PF14726 RTTN_N: Rotatin, an a 26.4 3E+02 0.0065 26.9 7.6 54 92-145 44-97 (98)
25 COG5096 Vesicle coat complex, 25.4 3.2E+02 0.007 35.2 9.6 108 19-146 37-154 (757)
26 smart00150 SPEC Spectrin repea 23.1 1.7E+02 0.0037 25.6 5.0 79 72-150 7-90 (101)
27 KOG2056 Equilibrative nucleosi 22.5 2E+02 0.0043 33.7 6.5 55 9-76 42-96 (336)
28 KOG0260 RNA polymerase II, lar 20.7 2.2E+03 0.049 29.8 15.4 64 10-84 662-725 (1605)
29 PF05589 DUF768: Protein of un 20.4 1.3E+02 0.0027 27.6 3.5 48 70-117 4-51 (64)
No 1
>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=99.16 E-value=6.9e-11 Score=105.50 Aligned_cols=57 Identities=26% Similarity=0.353 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhccCcc
Q 001649 95 EESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQGRV 151 (1038)
Q Consensus 95 ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~~v~ 151 (1038)
++.++.+|++|+++||+.+.|++++||++|+.|++|.+++|+++|+.|+++||+.+.
T Consensus 20 ~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 20 VSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 678999999999999999999999999999999999999999999999999998763
No 2
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.11 E-value=6.9e-11 Score=105.64 Aligned_cols=57 Identities=23% Similarity=0.313 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhccCcc
Q 001649 95 EESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQGRV 151 (1038)
Q Consensus 95 ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~~v~ 151 (1038)
++.++.+|++|+.+|++.+.|+++.||++|+.|++|+|++|+++|+.|++.||+.++
T Consensus 18 ~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 18 VSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 678999999999999999999999999999999999999999999999999999875
No 3
>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=99.03 E-value=1.3e-10 Score=96.77 Aligned_cols=52 Identities=31% Similarity=0.440 Sum_probs=47.1
Q ss_pred HHHHHHhhhccchhhhhccChHHHHhhhcCC-CCHHHHHHHHHHHHhhccCcc
Q 001649 100 AMMGALEKLHIDYELSVSSGIWITVKSLLGH-SSSQVQDRARALFDSWNQGRV 151 (1038)
Q Consensus 100 alL~ALekLPVd~e~Lks~~igktV~~L~~H-~n~~Iq~kAr~Lvd~Wk~~v~ 151 (1038)
.+|+.|++|||+.+.|++++||++|+.|++| .+++|+++|+.|+++||+.++
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 4799999999999999999999999999999 999999999999999998753
No 4
>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=98.55 E-value=5.3e-08 Score=106.96 Aligned_cols=59 Identities=17% Similarity=0.269 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhccCccCC
Q 001649 95 EESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQGRVSE 153 (1038)
Q Consensus 95 ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~~v~~~ 153 (1038)
++-++.+|+.|++++|+.+.|+++.||++|+.|++|.+.+|+++|+.||++||+.|..+
T Consensus 20 ~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~ 78 (299)
T TIGR01385 20 VEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKN 78 (299)
T ss_pred HHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhh
Confidence 56799999999999999999999999999999999999999999999999999998774
No 5
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=98.06 E-value=4.4e-06 Score=91.86 Aligned_cols=58 Identities=22% Similarity=0.328 Sum_probs=54.6
Q ss_pred HHHHHHHHHHhhhccchhhhhccChHHHHh-hhcCCCCHHHHHHHHHHHHhhccCccCC
Q 001649 96 ESITAMMGALEKLHIDYELSVSSGIWITVK-SLLGHSSSQVQDRARALFDSWNQGRVSE 153 (1038)
Q Consensus 96 e~ilalL~ALekLPVd~e~Lks~~igktV~-~L~~H~n~~Iq~kAr~Lvd~Wk~~v~~~ 153 (1038)
+-++.+|..|++.||+++.|+.+.||+.|+ .|++|+|++|.++|+.|++.||+++...
T Consensus 23 ~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~ 81 (296)
T KOG1105|consen 23 EAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS 81 (296)
T ss_pred HHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 578899999999999999999999999999 7779999999999999999999998864
No 6
>PLN02976 amine oxidase
Probab=97.85 E-value=3.7e-05 Score=98.19 Aligned_cols=102 Identities=20% Similarity=0.196 Sum_probs=87.6
Q ss_pred HHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhhccChHHHHhhhc
Q 001649 49 VVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSVSSGIWITVKSLL 128 (1038)
Q Consensus 49 ~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~ 128 (1038)
.+++.|+.--..+.-++.++-.||..||.||-+.- |++. .+||.-+|+.|--+|.|+.++..+||||||+.=.
T Consensus 1261 ~~~~~~~~~~~~~~~~~a~~~~gl~~l~~w~~~~~--~~~~-----~~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~ 1333 (1713)
T PLN02976 1261 HLAKELLNLPVETLKSFAGTKEGLATLNSWILDSM--GKDG-----TQLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKV 1333 (1713)
T ss_pred HHHHHHHhCCHHHHHHHhcccchHHHHHHHHHHHh--cccH-----HHHHHHHHHHHhhcchhHHHHHhccchHHHHhhh
Confidence 57777755555666778899999999999999984 4443 6899999999999999999999999999999875
Q ss_pred -CCCCHHHHHHHHHHHHhhccCccCCcccC
Q 001649 129 -GHSSSQVQDRARALFDSWNQGRVSEALDH 157 (1038)
Q Consensus 129 -~H~n~~Iq~kAr~Lvd~Wk~~v~~~~~~~ 157 (1038)
-|.+.+||..||.|++.|+++.+.+...+
T Consensus 1334 ~~h~~~~~r~~a~~~~~~w~~~~~~~~~~~ 1363 (1713)
T PLN02976 1334 CVHTSRDIRAIASQLVSVWLEVFRREKASN 1363 (1713)
T ss_pred hhcccHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 99999999999999999999977766543
No 7
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=97.29 E-value=8.3e-05 Score=85.93 Aligned_cols=138 Identities=10% Similarity=-0.042 Sum_probs=120.0
Q ss_pred cCCccchhhHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcC-----
Q 001649 13 KDGLTVPSRVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGN----- 87 (1038)
Q Consensus 13 kggL~~~~rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~----- 87 (1038)
+|++..-+.|..+..||+.+-+...+++ .. ...++.+|..+=.-+||-.|..|||..+..+|+++.+.+--
T Consensus 272 ~~~~~p~~~v~~~~~le~~s~~s~a~d~--~~--~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~ 347 (464)
T KOG1886|consen 272 QGSLWPNPSVSPCGALEQPSHASLAKDL--ES--YLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPDGQS 347 (464)
T ss_pred cccCCCCcccchhhhhhhhhhhhHhhhh--hh--hhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCCCcc
Confidence 5667778899999999999988755543 33 46889999888888999999999999999999999998332
Q ss_pred -CCCCchhHHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhccCccCCc
Q 001649 88 -NTNEGFVEESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQGRVSEA 154 (1038)
Q Consensus 88 -~~~d~~~ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~~v~~~~ 154 (1038)
...++-+.+....|+.+|+++++.++.+..+++++-++||..|.+++|...++++++.|+..+...+
T Consensus 348 ~~~~~~~~~d~~~~l~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~~~ 415 (464)
T KOG1886|consen 348 SPSSMKLNDDDYDGLCVGLELTAGSLYLYCGQEGLICAGHLPCPMLPEVKLSPVAAVHREGLLLAPSS 415 (464)
T ss_pred CccccccCchhHHHHHHhhhhhccchhhhcccccceeccccCCCCCCCcCcccccccchhhhccccee
Confidence 2234556788999999999999999999999999999999999999999999999999999987776
No 8
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.89 E-value=0.0015 Score=74.52 Aligned_cols=134 Identities=18% Similarity=0.242 Sum_probs=95.4
Q ss_pred hhHHHHHHHHhhcchh-hhhhhh--hhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchh--
Q 001649 20 SRVEELVGIMQKEKDF-VVKNIG--DATRQWAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFV-- 94 (1038)
Q Consensus 20 ~rV~eLvslMk~~k~~-v~kn~~--d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~-- 94 (1038)
.-|..|+..|+..-+. +..|.. -++..-.+|--+.+....+.+-+-||--|=|-.|..||-=.-. +|+
T Consensus 159 ~~v~~l~~~m~~aa~~D~~~N~e~kPA~~Klk~Lp~v~~vL~k~~L~et~LDngvL~~lk~WLePLPD-------~SLPa 231 (417)
T KOG1793|consen 159 DEVSRLMERMEDAAEKDRELNREGKPATQKLKLLPLVVAVLSKKALQETFLDNGVLDSLKEWLEPLPD-------GSLPA 231 (417)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccCchHHHHhccHHHHHHHhhhhHHHHHHhhhHHHHHHHHhccCCC-------CCCcc
Confidence 4566666677654221 222321 1333333455555666777888899999999999999975544 444
Q ss_pred HHHHHHHHHHHhhhccch-hhhhccChHHHHhhhcCCCC--HHHHHHHHHHHHhhccC-ccCCcccCCce
Q 001649 95 EESITAMMGALEKLHIDY-ELSVSSGIWITVKSLLGHSS--SQVQDRARALFDSWNQG-RVSEALDHDVK 160 (1038)
Q Consensus 95 ee~ilalL~ALekLPVd~-e~Lks~~igktV~~L~~H~n--~~Iq~kAr~Lvd~Wk~~-v~~~~~~~d~~ 160 (1038)
-..=.+||.+|..|||+. +||+.+|+|+.|=.|.+|.. ..++..|..||..|-.- ...++.-.|+-
T Consensus 232 l~Ir~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~~st~y~dm~ 301 (417)
T KOG1793|consen 232 LNIRKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFKLSTNYRDMR 301 (417)
T ss_pred hHHHHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccCCCCCchhhH
Confidence 234457899999999999 99999999999999998865 47899999999999887 44555444433
No 9
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=91.55 E-value=0.22 Score=55.86 Aligned_cols=76 Identities=20% Similarity=0.248 Sum_probs=55.9
Q ss_pred HHHHHHhcCCCCCchhHH--HHHHHHHHHhhhccchhhhhccChHHHHhhhc--CCCCHHHHHHHHHHHHhhccC-ccCC
Q 001649 79 LKQVQKFGNNTNEGFVEE--SITAMMGALEKLHIDYELSVSSGIWITVKSLL--GHSSSQVQDRARALFDSWNQG-RVSE 153 (1038)
Q Consensus 79 L~~aqk~g~~~~d~~~ee--~ilalL~ALekLPVd~e~Lks~~igktV~~L~--~H~n~~Iq~kAr~Lvd~Wk~~-v~~~ 153 (1038)
|+..+.|=.--.|+++.. .---||-+|.+|||--+||+.+|||++|=... +....+|+..|.+||..|..- ++.+
T Consensus 211 LdsVr~WLEPLPD~SlP~~~IqksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIik~s 290 (397)
T COG5139 211 LDSVRGWLEPLPDKSLPNIKIQKSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIKPS 290 (397)
T ss_pred HHHHHhhhccCCCCCCcchHHHHHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccccCcC
Confidence 344444433334555533 33457888999999999999999999997764 777889999999999999876 4444
Q ss_pred c
Q 001649 154 A 154 (1038)
Q Consensus 154 ~ 154 (1038)
.
T Consensus 291 ~ 291 (397)
T COG5139 291 G 291 (397)
T ss_pred C
Confidence 3
No 10
>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=82.29 E-value=11 Score=33.95 Aligned_cols=105 Identities=20% Similarity=0.270 Sum_probs=63.2
Q ss_pred hHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchhHHHHHH
Q 001649 21 RVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFVEESITA 100 (1038)
Q Consensus 21 rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ila 100 (1038)
.|+.|+.+|+.....++.+. +..++++.. .++++...|++.+++..|-.-|.+ .+ .++...
T Consensus 8 ~i~~l~~~l~~~~~~~~~~a------~~~l~~l~~--~~~~~~~~~~~~~~i~~l~~~l~~-------~~----~~v~~~ 68 (120)
T cd00020 8 GLPALVSLLSSSDENVQREA------AWALSNLSA--GNNDNIQAVVEAGGLPALVQLLKS-------ED----EEVVKA 68 (120)
T ss_pred ChHHHHHHHHcCCHHHHHHH------HHHHHHHhc--CCHHHHHHHHHCCChHHHHHHHhC-------CC----HHHHHH
Confidence 58889999986653333222 223444332 248899999999999888777764 11 223444
Q ss_pred HHHHHhhhc----cchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHH
Q 001649 101 MMGALEKLH----IDYELSVSSGIWITVKSLLGHSSSQVQDRARALFD 144 (1038)
Q Consensus 101 lL~ALekLP----Vd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd 144 (1038)
.+.+|-.|= -..+.+...|+-+.+-++....+.+++..|-.++.
T Consensus 69 a~~~L~~l~~~~~~~~~~~~~~g~l~~l~~~l~~~~~~~~~~a~~~l~ 116 (120)
T cd00020 69 ALWALRNLAAGPEDNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGALS 116 (120)
T ss_pred HHHHHHHHccCcHHHHHHHHHCCChHHHHHHHhcCCHHHHHHHHHHHH
Confidence 444444442 22334445555555555666668899998877764
No 11
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=76.97 E-value=0.92 Score=53.27 Aligned_cols=57 Identities=19% Similarity=0.169 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhccCccCCc
Q 001649 96 ESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQGRVSEA 154 (1038)
Q Consensus 96 e~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~~v~~~~ 154 (1038)
.=++.-|.-|-+||+...+|.+.+++|+|+.|++|. .+-+.|+.|+..||+.+..+-
T Consensus 25 kR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d~ 81 (433)
T KOG2821|consen 25 KRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVDF 81 (433)
T ss_pred HHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhccccc
Confidence 346667788889999999999999999999999998 799999999999999865544
No 12
>PHA02763 hypothetical protein; Provisional
Probab=65.52 E-value=7 Score=37.56 Aligned_cols=41 Identities=17% Similarity=0.588 Sum_probs=32.2
Q ss_pred HHHHHh-hccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCC
Q 001649 50 VASALS-ATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTN 90 (1038)
Q Consensus 50 ~a~~ia-aTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~ 90 (1038)
.+.+|| |--..|||+.||+..|..-++.||.+|+..-++.-
T Consensus 44 ~gKvIa~ap~t~~~LsKYv~~SGFe~VEeWl~eArrLh~~~i 85 (102)
T PHA02763 44 PGKVIAKAPVTEYCLSKYVKFSGFENVEEWLNEARRLHNDKI 85 (102)
T ss_pred cceEEEecCchHHHHHHHhhhcchhhHHHHHHHHHHHhcCCC
Confidence 344444 22356999999999999999999999999776544
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=60.23 E-value=39 Score=34.02 Aligned_cols=93 Identities=15% Similarity=0.133 Sum_probs=55.9
Q ss_pred HHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCC-CCchhHHHHHHHHHHHhhhccchhhhhc-cChHHHHhhhc
Q 001649 51 ASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNT-NEGFVEESITAMMGALEKLHIDYELSVS-SGIWITVKSLL 128 (1038)
Q Consensus 51 a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~-~d~~~ee~ilalL~ALekLPVd~e~Lks-~~igktV~~L~ 128 (1038)
..+..-|++-+=++.||..+|+.+|-.+|.......... .+..++-.++.-|+||-.-..-++.+.. .++-.++-..+
T Consensus 88 L~v~Lrt~~~~Wv~~Fl~~~G~~~L~~~L~~~~~~~~~~~~~~~~~~~~l~Clkal~n~~~G~~~v~~~~~~v~~i~~~L 167 (187)
T PF06371_consen 88 LRVSLRTNPISWVQEFLELGGLEALLNVLSKLNKKKEKSEEDIDIEHECLRCLKALMNTKYGLEAVLSHPDSVNLIALSL 167 (187)
T ss_dssp HHHHHHHS-HHHHHHH-HHHHHHHHHHHHHHHHTHHCTCTTCHHHHHHHHHHHHHHTSSHHHHHHHHCSSSHHHHHHHT-
T ss_pred HHHHhccCCchHHHHhccCCCHHHHHHHHHHhhhhhhhcchhHHHHHHHHHHHHHHHccHHHHHHHHcCcHHHHHHHHHH
Confidence 344555667778999999999999999999988743322 3333344444445555554544444443 33333333334
Q ss_pred CCCCHHHHHHHHHHH
Q 001649 129 GHSSSQVQDRARALF 143 (1038)
Q Consensus 129 ~H~n~~Iq~kAr~Lv 143 (1038)
...+.+++..|-.|+
T Consensus 168 ~s~~~~~r~~~leiL 182 (187)
T PF06371_consen 168 DSPNIKTRKLALEIL 182 (187)
T ss_dssp -TTSHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHH
Confidence 567788888887765
No 14
>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=53.80 E-value=14 Score=36.28 Aligned_cols=55 Identities=15% Similarity=0.192 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhhccchhhhhc-cChHHHHhhhc-CCCCHHHHHHHHHHHHhhccCcc
Q 001649 97 SITAMMGALEKLHIDYELSVS-SGIWITVKSLL-GHSSSQVQDRARALFDSWNQGRV 151 (1038)
Q Consensus 97 ~ilalL~ALekLPVd~e~Lks-~~igktV~~L~-~H~n~~Iq~kAr~Lvd~Wk~~v~ 151 (1038)
--+.+|.-|..|||+...|+. ..+-.|+++|| =-.|..|+++|..|+.+.|.+.-
T Consensus 24 kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 24 KCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp HHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence 446788899999999999996 67888999997 34568999999999999999964
No 15
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=43.11 E-value=79 Score=39.22 Aligned_cols=81 Identities=17% Similarity=0.272 Sum_probs=48.3
Q ss_pred HHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhhccChHHHHhh
Q 001649 47 WAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSVSSGIWITVKS 126 (1038)
Q Consensus 47 ~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lks~~igktV~~ 126 (1038)
|-++|..|.---.-|.-+++++|-=+-|||.||-..|. +-.++++.+|-+.+ .-+.|----.|.
T Consensus 139 ~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqr-------k~~~~~~~~l~~~v--------~~~yc~~~~~~~- 202 (757)
T KOG4368|consen 139 CELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQR-------KQARELLAALQKVV--------VPIYCTSFLAVE- 202 (757)
T ss_pred HHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHh--------HHHHHhhhhhhH-
Confidence 33455555444445677788888889999999999887 44344443333322 122332222222
Q ss_pred hcCCCCHHHHHHHHHHHHhhccC
Q 001649 127 LLGHSSSQVQDRARALFDSWNQG 149 (1038)
Q Consensus 127 L~~H~n~~Iq~kAr~Lvd~Wk~~ 149 (1038)
+.-+++-..|+.-|-+.
T Consensus 203 ------e~~~~~~~~ll~~we~~ 219 (757)
T KOG4368|consen 203 ------EDKQQKIARLLQLWEKN 219 (757)
T ss_pred ------hHHHHHHHHHHHHHhhc
Confidence 33567777788899776
No 16
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.85 E-value=84 Score=38.50 Aligned_cols=112 Identities=14% Similarity=0.231 Sum_probs=69.1
Q ss_pred hHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchhHHHHHH
Q 001649 21 RVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFVEESITA 100 (1038)
Q Consensus 21 rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ila 100 (1038)
=++.||++|+.......|-. . |+ -.-+.+.-+++-+...|+.|=+.=|=.-| .| -|. ..|..
T Consensus 365 l~p~Li~~l~~~ef~~rKEA---a--wa--IsN~ts~g~~~qi~yLv~~giI~plcdlL----~~----~D~---~ii~v 426 (514)
T KOG0166|consen 365 LIPVLINLLQTAEFDIRKEA---A--WA--ISNLTSSGTPEQIKYLVEQGIIKPLCDLL----TC----PDV---KIILV 426 (514)
T ss_pred cHHHHHHHHhccchHHHHHH---H--HH--HHhhcccCCHHHHHHHHHcCCchhhhhcc----cC----CCh---HHHHH
Confidence 37889999998765444422 1 42 23444555677777777777444333333 21 112 23455
Q ss_pred HHHHHhh-------hcc----chh-hhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhccCc
Q 001649 101 MMGALEK-------LHI----DYE-LSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQGR 150 (1038)
Q Consensus 101 lL~ALek-------LPV----d~e-~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~~v 150 (1038)
+|.||+. ..- -+. .+..||.---...|..|+|.+|-++|..|+++.-...
T Consensus 427 ~Ld~l~nil~~~e~~~~~~~n~~~~~IEe~ggldkiE~LQ~hen~~Iy~~A~~II~~yf~~e 488 (514)
T KOG0166|consen 427 ALDGLENILKVGEAEKNRGTNPLAIMIEEAGGLDKIENLQSHENEEIYKKAYKIIDTYFSEE 488 (514)
T ss_pred HHHHHHHHHHHHHHhccccccHHHHHHHHccChhHHHHhhccccHHHHHHHHHHHHHhcCCC
Confidence 5544443 331 112 2336788888899999999999999999999987664
No 17
>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=42.28 E-value=44 Score=29.00 Aligned_cols=59 Identities=14% Similarity=0.188 Sum_probs=41.3
Q ss_pred cCchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhcc
Q 001649 69 LDGLGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWNQ 148 (1038)
Q Consensus 69 l~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk~ 148 (1038)
|..|-++|..||.+++-+. +. ++. .-+..+..++.++....+.+++++...|++-|++
T Consensus 2 L~~lYl~ndI~q~sk~k~~---~~----f~~---------------~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~ 59 (64)
T PF04818_consen 2 LALLYLANDILQNSKRKNP---DE----FAP---------------AFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEE 59 (64)
T ss_dssp HHHHHHHHHHHHHHHHHTT---HC----HHH---------------HHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHH
T ss_pred cceeehHHHHHHHhhhcCh---HH----HHH---------------HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhC
Confidence 4567889999999987221 11 221 1234556677777777799999999999999987
Q ss_pred C
Q 001649 149 G 149 (1038)
Q Consensus 149 ~ 149 (1038)
+
T Consensus 60 r 60 (64)
T PF04818_consen 60 R 60 (64)
T ss_dssp C
T ss_pred C
Confidence 6
No 18
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=40.73 E-value=1.8e+02 Score=28.65 Aligned_cols=112 Identities=12% Similarity=0.222 Sum_probs=61.3
Q ss_pred hhhhhhhhHHHHHHHHhhccch--hHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhh
Q 001649 39 NIGDATRQWAVVASALSATENR--DCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSV 116 (1038)
Q Consensus 39 n~~d~~rq~~~~a~~iaaTen~--DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lk 116 (1038)
.+..+..+|..|-..+..-... +++...-.+..+.-|..||.++...=.......=.+.|..+|+.++.|--++...+
T Consensus 80 ~~~~l~~~w~~l~~~~~~r~~~L~~~~~~~~~~~~~~~l~~wl~~~e~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 159 (213)
T cd00176 80 RLEELNQRWEELRELAEERRQRLEEALDLQQFFRDADDLEQWLEEKEAALASEDLGKDLESVEELLKKHKELEEELEAHE 159 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHhch
Confidence 3334444555544444333322 44444444455555999999988732211100013466667777776665554322
Q ss_pred c-----cChHHHHhhhcCCCC-HHHHHHHHHHHHhhccCc
Q 001649 117 S-----SGIWITVKSLLGHSS-SQVQDRARALFDSWNQGR 150 (1038)
Q Consensus 117 s-----~~igktV~~L~~H~n-~~Iq~kAr~Lvd~Wk~~v 150 (1038)
. ...+.-+..+..+.. ..|+.+...|...|..+.
T Consensus 160 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~~l~ 199 (213)
T cd00176 160 PRLKSLNELAEELLEEGHPDADEEIEEKLEELNERWEELL 199 (213)
T ss_pred HHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 1 222333333334444 789999999999998763
No 19
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=37.85 E-value=2e+02 Score=29.97 Aligned_cols=87 Identities=22% Similarity=0.168 Sum_probs=53.2
Q ss_pred hhHHHHHHhcCc--hHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhhcc----ChHHHHhhhcCCCCH
Q 001649 60 RDCLDRFIQLDG--LGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSVSS----GIWITVKSLLGHSSS 133 (1038)
Q Consensus 60 ~DcL~~FIql~G--l~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lks~----~igktV~~L~~H~n~ 133 (1038)
..||.-+++.-+ -.++-.=|..+.+ . -|-......+.-|..+|+..+.+...+... .+.+.+.+++...++
T Consensus 115 ~~~L~~i~~~~~~~~~~~~~~l~~~~~-~--Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D~~~ 191 (228)
T PF12348_consen 115 NNALDAIIESCSYSPKILLEILSQGLK-S--KNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKALVKLLSDADP 191 (228)
T ss_dssp HHHHHHHHTTS-H--HHHHHHHHHHTT----S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHHHHHHTSS-H
T ss_pred HHHHHHHHHHCCcHHHHHHHHHHHHHh-C--CCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHHHHHCCCCCH
Confidence 367777777766 3333444444443 2 222334667777888889999666666654 478888888899999
Q ss_pred HHHHHHHHHHHhhccC
Q 001649 134 QVQDRARALFDSWNQG 149 (1038)
Q Consensus 134 ~Iq~kAr~Lvd~Wk~~ 149 (1038)
+||+.||.++....+.
T Consensus 192 ~VR~~Ar~~~~~l~~~ 207 (228)
T PF12348_consen 192 EVREAARECLWALYSH 207 (228)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999888655
No 20
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=36.77 E-value=95 Score=31.34 Aligned_cols=41 Identities=15% Similarity=0.076 Sum_probs=30.2
Q ss_pred hhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhhc
Q 001649 107 KLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSWN 147 (1038)
Q Consensus 107 kLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~Wk 147 (1038)
..|--...+..-|+-..|=.|..|.|++||..|-.-+.+|+
T Consensus 74 ~~p~gr~ii~~lg~K~~vM~Lm~h~d~eVr~eAL~avQklm 114 (119)
T PF11698_consen 74 HYPNGRNIIEKLGAKERVMELMNHEDPEVRYEALLAVQKLM 114 (119)
T ss_dssp H-GGGHHHHHHHSHHHHHHHHTS-SSHHHHHHHHHHHHHHH
T ss_pred HChhHHHHHHhcChHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence 34555556666777777888999999999999987777665
No 21
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=34.48 E-value=3.3e+02 Score=30.46 Aligned_cols=91 Identities=16% Similarity=0.121 Sum_probs=62.0
Q ss_pred HHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhcc--chhhhhccChHHHH
Q 001649 47 WAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHI--DYELSVSSGIWITV 124 (1038)
Q Consensus 47 ~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPV--d~e~Lks~~igktV 124 (1038)
+-++.-+=.=|=++++...|.+-+=+..|-+=++.++| -.|-.+.+++|+=|-.-.. ....+..|++-+++
T Consensus 216 Y~~ll~lWlLSF~~~~~~~~~~~~~i~~L~~i~~~~~K-------EKvvRv~la~l~Nl~~~~~~~~~~~mv~~~~l~~l 288 (312)
T PF03224_consen 216 YQALLCLWLLSFEPEIAEELNKKYLIPLLADILKDSIK-------EKVVRVSLAILRNLLSKAPKSNIELMVLCGLLKTL 288 (312)
T ss_dssp HHHHHHHHHHTTSHHHHHHHHTTSHHHHHHHHHHH--S-------HHHHHHHHHHHHHTTSSSSTTHHHHHHHH-HHHHH
T ss_pred HHHHHHHHHHhcCHHHHHHHhccchHHHHHHHHHhccc-------chHHHHHHHHHHHHHhccHHHHHHHHHHccHHHHH
Confidence 33333444456778888888888866667777777777 3455677777777766676 67778899999999
Q ss_pred hhh--cCCCCHHHHHHHHHHHH
Q 001649 125 KSL--LGHSSSQVQDRARALFD 144 (1038)
Q Consensus 125 ~~L--~~H~n~~Iq~kAr~Lvd 144 (1038)
++| |+..+++|.+--..|-+
T Consensus 289 ~~L~~rk~~Dedl~edl~~L~e 310 (312)
T PF03224_consen 289 QNLSERKWSDEDLTEDLEFLKE 310 (312)
T ss_dssp HHHHSS--SSHHHHHHHHHHHH
T ss_pred HHHhcCCCCCHHHHHHHHHHHh
Confidence 999 58899999876665544
No 22
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=32.84 E-value=19 Score=39.68 Aligned_cols=42 Identities=29% Similarity=0.339 Sum_probs=33.1
Q ss_pred CCCchhHHHHHHHHHHHh-hhccchhhhhccChHHHHhhhcCCCC
Q 001649 89 TNEGFVEESITAMMGALE-KLHIDYELSVSSGIWITVKSLLGHSS 132 (1038)
Q Consensus 89 ~~d~~~ee~ilalL~ALe-kLPVd~e~Lks~~igktV~~L~~H~n 132 (1038)
|.+..|-+-|.|+|.|-+ .||||++.= -.+|-+.+|||.|.|
T Consensus 100 TISAKvm~~ikavLgaTKiDLPVDINDP--YDlGLLLRhLRHHSN 142 (238)
T PF02084_consen 100 TISAKVMEDIKAVLGATKIDLPVDINDP--YDLGLLLRHLRHHSN 142 (238)
T ss_pred cccHHHHHHHHHHhcccccccccccCCh--hhHHHHHHHHHHHHH
Confidence 344566778999998876 799998754 457889999999987
No 23
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=27.56 E-value=1.6e+02 Score=41.78 Aligned_cols=132 Identities=16% Similarity=0.094 Sum_probs=0.0
Q ss_pred ccccccccccccCCccchhhHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHH
Q 001649 2 TLEDFFSLTKMKDGLTVPSRVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQ 81 (1038)
Q Consensus 2 tleDFftLtemkggL~~~~rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~ 81 (1038)
.|+-++.-.|.+-.+..-..|..||.+|+.....+++|. +.+++.....---.|.|..+++-.|.-.==-=|-.
T Consensus 717 ALanLl~~~e~~~ei~~~~~I~~Lv~lLr~G~~~~k~~A------a~AL~~L~~~~~~~~~~~~~~~~~g~v~~l~~~L~ 790 (2102)
T PLN03200 717 ALANLLSDPEVAAEALAEDIILPLTRVLREGTLEGKRNA------ARALAQLLKHFPVDDVLKDSVQCRGTVLALVDLLN 790 (2102)
T ss_pred HHHHHHcCchHHHHHHhcCcHHHHHHHHHhCChHHHHHH------HHHHHHHHhCCChhHHHHHHHHHhCcHHHHHHHHh
Q ss_pred HHHhcCCCCCchhHHHHHHHHHHHhhh---------ccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHh
Q 001649 82 VQKFGNNTNEGFVEESITAMMGALEKL---------HIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDS 145 (1038)
Q Consensus 82 aqk~g~~~~d~~~ee~ilalL~ALekL---------PVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~ 145 (1038)
+.+ .+...---.+..|..|-+. |...-.=.-.++.++|..| .|.++.||+||-.++.+
T Consensus 791 ~~~-----~~~~~~~~al~~l~~l~~~~~~~~~~~~~~~~~~e~p~~l~~l~~~l-~~~~p~~~~kai~il~~ 857 (2102)
T PLN03200 791 STD-----LDSSATSEALEALALLARTKGGANFSHPPWAVLAEVPSSLEPLVRCL-AEGHPLVQDKAIEILSR 857 (2102)
T ss_pred cCC-----cchhhHHHHHHHHHHHHhhcccCCCCCCchhhHHhccCchHHHHHHH-HcCChHHHHHHHHHHHH
No 24
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=26.42 E-value=3e+02 Score=26.92 Aligned_cols=54 Identities=15% Similarity=0.107 Sum_probs=48.4
Q ss_pred chhHHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHh
Q 001649 92 GFVEESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDS 145 (1038)
Q Consensus 92 ~~~ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~ 145 (1038)
.+.++-+++||.-|-+-|--...|..-|.-....+|+.+-++..+...-.|++.
T Consensus 44 ~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~~ 97 (98)
T PF14726_consen 44 VPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILDQ 97 (98)
T ss_pred CccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHhc
Confidence 456889999999999999999999999999999999999999999988887764
No 25
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=25.40 E-value=3.2e+02 Score=35.20 Aligned_cols=108 Identities=20% Similarity=0.247 Sum_probs=67.1
Q ss_pred hhhHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhH---HHHHH----hcCc---hHHHHHHHHHHHHhcCC
Q 001649 19 PSRVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDC---LDRFI----QLDG---LGLIDRWLKQVQKFGNN 88 (1038)
Q Consensus 19 ~~rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~Dc---L~~FI----ql~G---l~~L~~WL~~aqk~g~~ 88 (1038)
.+++.++|+.|....++-.. |.-|...++ |++.|. +.+|+ ++.+ +..+|.-++++|.
T Consensus 37 idAmK~iIa~M~~G~dmssL--------f~dViK~~~-trd~ElKrL~ylYl~~yak~~P~~~lLavNti~kDl~d---- 103 (757)
T COG5096 37 IDAMKKIIAQMSLGEDMSSL--------FPDVIKNVA-TRDVELKRLLYLYLERYAKLKPELALLAVNTIQKDLQD---- 103 (757)
T ss_pred HHHHHHHHHHHhcCCChHHH--------HHHHHHHHH-hcCHHHHHHHHHHHHHHhccCHHHHHHHHHHHHhhccC----
Confidence 57889999999988876443 223333344 666665 22222 2222 3445555555555
Q ss_pred CCCchhHHHHHHHHHHHhhhccchhhhhccChHHHHhhhcCCCCHHHHHHHHHHHHhh
Q 001649 89 TNEGFVEESITAMMGALEKLHIDYELSVSSGIWITVKSLLGHSSSQVQDRARALFDSW 146 (1038)
Q Consensus 89 ~~d~~~ee~ilalL~ALekLPVd~e~Lks~~igktV~~L~~H~n~~Iq~kAr~Lvd~W 146 (1038)
.| |+.=-.-||+|=+|.+. +. -..+-.+|+++..|.+..||+.|..=+-+-
T Consensus 104 ~N----~~iR~~AlR~ls~l~~~-el--~~~~~~~ik~~l~d~~ayVRk~Aalav~kl 154 (757)
T COG5096 104 PN----EEIRGFALRTLSLLRVK-EL--LGNIIDPIKKLLTDPHAYVRKTAALAVAKL 154 (757)
T ss_pred CC----HHHHHHHHHHHHhcChH-HH--HHHHHHHHHHHccCCcHHHHHHHHHHHHHH
Confidence 22 44444567888887743 22 246788999999999999999987544443
No 26
>smart00150 SPEC Spectrin repeats.
Probab=23.07 E-value=1.7e+02 Score=25.57 Aligned_cols=79 Identities=16% Similarity=0.300 Sum_probs=47.6
Q ss_pred hHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhhc--cChHHHHhhhc---CCCCHHHHHHHHHHHHhh
Q 001649 72 LGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSVS--SGIWITVKSLL---GHSSSQVQDRARALFDSW 146 (1038)
Q Consensus 72 l~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lks--~~igktV~~L~---~H~n~~Iq~kAr~Lvd~W 146 (1038)
+.-|..||.++...-....-..=.+.+-.+|+.++.|--+++..+. ..+-.+-..|. ......|+.+...|-..|
T Consensus 7 ~~~l~~Wl~~~e~~l~~~~~~~d~~~~~~~~~~~~~~~~e~~~~~~~v~~~~~~~~~L~~~~~~~~~~i~~~~~~l~~~w 86 (101)
T smart00150 7 ADELEAWLSEKEALLASEDLGKDLESVEALLKKHEALEAELEAHEERVEALNELGEQLIEEGHPDAEEIEERLEELNERW 86 (101)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHH
Confidence 4456789998875322111111145666777777777666655443 23333444443 345567999999999999
Q ss_pred ccCc
Q 001649 147 NQGR 150 (1038)
Q Consensus 147 k~~v 150 (1038)
..+.
T Consensus 87 ~~l~ 90 (101)
T smart00150 87 EELK 90 (101)
T ss_pred HHHH
Confidence 8763
No 27
>KOG2056 consensus Equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=22.54 E-value=2e+02 Score=33.74 Aligned_cols=55 Identities=16% Similarity=0.331 Sum_probs=33.7
Q ss_pred cccccCCccchhhHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHH
Q 001649 9 LTKMKDGLTVPSRVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDCLDRFIQLDGLGLID 76 (1038)
Q Consensus 9 LtemkggL~~~~rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~ 76 (1038)
|+||-.+=-....+.||+.++-+-.+ +.-+.|..|.+.| -+|++.|.-|--+|++
T Consensus 42 m~eIA~~ty~~~e~~eIm~vi~kRl~-------d~gknWR~VyKaL------tlleyLl~~GSErv~~ 96 (336)
T KOG2056|consen 42 MAEIAQATYNFVEYQEIMDVLWKRLN-------DSGKNWRHVYKAL------TLLEYLLKNGSERVVD 96 (336)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHHHh-------hccchHHHHHHHH------HHHHHHHhcCcHHHHH
Confidence 44554444556667788888775522 3445577777777 4677777755554443
No 28
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=20.66 E-value=2.2e+03 Score=29.84 Aligned_cols=64 Identities=16% Similarity=0.236 Sum_probs=41.9
Q ss_pred ccccCCccchhhHHHHHHHHhhcchhhhhhhhhhhhhHHHHHHHHhhccchhHHHHHHhcCchHHHHHHHHHHHH
Q 001649 10 TKMKDGLTVPSRVEELVGIMQKEKDFVVKNIGDATRQWAVVASALSATENRDCLDRFIQLDGLGLIDRWLKQVQK 84 (1038)
Q Consensus 10 temkggL~~~~rV~eLvslMk~~k~~v~kn~~d~~rq~~~~a~~iaaTen~DcL~~FIql~Gl~~L~~WL~~aqk 84 (1038)
.+|.|+|.+.+-|.++=++|++.+..|. +++++ +..+-|..|--.-.+.-|.. .+++-|++|..
T Consensus 662 igIgDtiad~~t~~~iq~~I~~ak~dv~----~vi~~--a~~~~L~~~pg~tlretfe~-----~v~~vlndArd 725 (1605)
T KOG0260|consen 662 IGIGDTIADAATMCVIQNTIKEAKRDVL----AVIRE--AQNNELEPTPGRTLRETFEN-----KVNRVLNDARD 725 (1605)
T ss_pred ccccccccCHHHHHHHHHHHHHHHHHHH----HHHHH--HhhccccCCcchhHHHHHHH-----HHHHHHHHHHH
Confidence 3689999999999999999999987755 34443 34444443333333444543 35666676665
No 29
>PF05589 DUF768: Protein of unknown function (DUF768); InterPro: IPR008486 This family consists of several uncharacterised hypothetical proteins from Rhizobium loti (Mesorhizobium loti).
Probab=20.36 E-value=1.3e+02 Score=27.63 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=34.5
Q ss_pred CchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHhhhccchhhhhc
Q 001649 70 DGLGLIDRWLKQVQKFGNNTNEGFVEESITAMMGALEKLHIDYELSVS 117 (1038)
Q Consensus 70 ~Gl~~L~~WL~~aqk~g~~~~d~~~ee~ilalL~ALekLPVd~e~Lks 117 (1038)
+|..||++|+.+=--+.-...--++.+|-..++.+-+++-|..+-+..
T Consensus 4 r~~~Fl~~WI~e~V~~~~~~d~is~~~La~kl~adA~a~Gi~~~ei~e 51 (64)
T PF05589_consen 4 RGIEFLDSWIAENVPDTPKADIISAAELAEKLFADAEAAGIPREEIEE 51 (64)
T ss_pred hHHHHHHHHHHhcCCCccccchhhHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 688999999987554332222245688888899999999888777543
Done!