Query 025285
Match_columns 255
No_of_seqs 151 out of 432
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:18:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025285.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025285hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2606 OTU (ovarian tumor)-li 99.8 9.1E-20 2E-24 168.6 5.2 80 7-88 213-299 (302)
2 PF02338 OTU: OTU-like cystein 98.9 1.3E-09 2.9E-14 85.4 4.8 56 26-81 56-121 (121)
3 KOG3288 OTU-like cysteine prot 98.5 2.7E-08 5.9E-13 92.0 0.8 66 18-85 165-231 (307)
4 COG5539 Predicted cysteine pro 98.0 3.3E-06 7.1E-11 79.2 3.7 65 18-86 236-306 (306)
5 KOG2605 OTU (ovarian tumor)-li 97.7 3.2E-05 6.8E-10 74.6 4.1 71 17-87 270-344 (371)
6 PF10275 Peptidase_C65: Peptid 97.5 0.00022 4.7E-09 63.6 6.1 69 16-85 167-243 (244)
7 cd00194 UBA Ubiquitin Associat 97.2 0.00048 1E-08 44.8 4.0 37 206-242 2-38 (38)
8 PF00627 UBA: UBA/TS-N domain; 97.1 0.001 2.2E-08 43.8 4.3 35 206-240 3-37 (37)
9 smart00165 UBA Ubiquitin assoc 96.7 0.0026 5.7E-08 41.2 3.9 36 206-241 2-37 (37)
10 KOG3991 Uncharacterized conser 96.1 0.0092 2E-07 55.1 5.0 76 9-85 169-254 (256)
11 COG5539 Predicted cysteine pro 93.3 0.012 2.6E-07 55.7 -1.9 65 18-85 164-230 (306)
12 TIGR00601 rad23 UV excision re 91.1 0.63 1.4E-05 45.3 6.8 42 200-241 151-192 (378)
13 KOG0011 Nucleotide excision re 88.5 1 2.2E-05 43.6 5.8 43 199-241 129-171 (340)
14 TIGR00601 rad23 UV excision re 87.1 0.81 1.8E-05 44.5 4.4 43 202-244 334-376 (378)
15 PF09288 UBA_3: Fungal ubiquit 83.8 1.1 2.4E-05 33.0 2.7 26 205-230 9-34 (55)
16 KOG2561 Adaptor protein NUB1, 66.3 11 0.00023 38.6 5.1 45 201-245 425-469 (568)
17 KOG0011 Nucleotide excision re 60.7 12 0.00026 36.5 4.2 43 202-244 295-337 (340)
18 COG5207 UBP14 Isopeptidase T [ 57.0 14 0.00031 38.5 4.2 38 206-243 559-597 (749)
19 KOG2605 OTU (ovarian tumor)-li 52.8 3.2 7E-05 40.6 -1.0 41 121-161 298-338 (371)
20 KOG0944 Ubiquitin-specific pro 41.9 23 0.0005 37.7 3.1 39 203-241 633-671 (763)
21 PF05801 DUF840: Lagovirus pro 36.7 50 0.0011 27.2 3.6 34 94-134 5-38 (114)
22 PF05697 Trigger_N: Bacterial 35.3 85 0.0018 25.7 4.9 45 95-160 38-82 (145)
23 PTZ00250 variable surface prot 28.5 33 0.00072 33.4 1.6 18 226-243 264-281 (350)
24 KOG1252 Cystathionine beta-syn 28.2 1.1E+02 0.0023 30.4 5.0 107 14-127 181-298 (362)
25 TIGR03142 cytochro_ccmI cytoch 25.9 1.7E+02 0.0036 23.6 5.0 47 105-151 30-76 (117)
26 KOG0944 Ubiquitin-specific pro 21.8 1.7E+02 0.0037 31.5 5.3 39 205-243 571-610 (763)
27 PF02845 CUE: CUE domain; Int 21.6 2.5E+02 0.0054 18.5 4.8 37 207-243 3-41 (42)
28 PF07499 RuvA_C: RuvA, C-termi 21.3 1.3E+02 0.0028 20.6 3.1 26 204-229 2-27 (47)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.78 E-value=9.1e-20 Score=168.64 Aligned_cols=80 Identities=24% Similarity=0.420 Sum_probs=67.0
Q ss_pred ccccCCCCcc-hHHHHHcccCCC-CCCCHHHHHHHHHhhCCCEEEEecCCCceeEecCCCCCCCCCEEEEecC-----CC
Q 025285 7 SVCNCDSHSF-VVKRFVLTSWMQ-VYGNNVEIQALCEMYNRPIHIYSYTTEPINIFHGSYNTDNPPIRLSYHH-----GN 79 (255)
Q Consensus 7 ~~~n~Df~~y-~fdeYc~rird~-~WGG~iELqALSelynrpI~Vyq~~~~pI~if~~e~~~~~~pI~LSYH~-----Ge 79 (255)
-.++.|..++ .|++||+.|+++ +|||+|||+|||++|.+||+||+.++++ .+++++|.+ .+||+|+||+ |+
T Consensus 213 ~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p~-~~~geey~k-d~pL~lvY~rH~y~LGe 290 (302)
T KOG2606|consen 213 DEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGPI-LEYGEEYGK-DKPLILVYHRHAYGLGE 290 (302)
T ss_pred CccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCCc-eeechhhCC-CCCeeeehHHhHHHHHh
Confidence 3444444333 399999999998 9999999999999999999999999775 556688875 6899999999 99
Q ss_pred CcccccCCC
Q 025285 80 HYNSLVDPR 88 (255)
Q Consensus 80 HYNSV~~~~ 88 (255)
||||+.++.
T Consensus 291 HYNS~~~~~ 299 (302)
T KOG2606|consen 291 HYNSVTPLK 299 (302)
T ss_pred hhccccccc
Confidence 999998654
No 2
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=98.92 E-value=1.3e-09 Score=85.40 Aligned_cols=56 Identities=41% Similarity=0.707 Sum_probs=43.2
Q ss_pred CCCCCCCHHHHHHHHHhhCCCEEEEecCCCceeEe---cC--CCCCCCCCEEEEecC-----CCCc
Q 025285 26 WMQVYGNNVEIQALCEMYNRPIHIYSYTTEPINIF---HG--SYNTDNPPIRLSYHH-----GNHY 81 (255)
Q Consensus 26 rd~~WGG~iELqALSelynrpI~Vyq~~~~pI~if---~~--e~~~~~~pI~LSYH~-----GeHY 81 (255)
++++|||++||+|||++|++||.||+........+ .+ ......++|+|+|+. ++||
T Consensus 56 ~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 56 KPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp STTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred cccccCcHHHHHHHHHHhCCeEEEEEcCCCCccceeeecCccccCCCCCeEEEEEcCCccCCCCCC
Confidence 45599999999999999999999998755432222 11 112357899999999 9998
No 3
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=2.7e-08 Score=92.02 Aligned_cols=66 Identities=26% Similarity=0.373 Sum_probs=53.9
Q ss_pred HHHHHcccCCC-CCCCHHHHHHHHHhhCCCEEEEecCCCceeEecCCCCCCCCCEEEEecCCCCccccc
Q 025285 18 VKRFVLTSWMQ-VYGNNVEIQALCEMYNRPIHIYSYTTEPINIFHGSYNTDNPPIRLSYHHGNHYNSLV 85 (255)
Q Consensus 18 fdeYc~rird~-~WGG~iELqALSelynrpI~Vyq~~~~pI~if~~e~~~~~~pI~LSYH~GeHYNSV~ 85 (255)
=.+||.+|++. .|||.|||..||..|++-|.|+..++..|.-|++.-+-++ -+.|. +.|.||+++.
T Consensus 165 n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt~rid~fged~~~~~-rv~ll-ydGIHYD~l~ 231 (307)
T KOG3288|consen 165 NKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQTVRIDRFGEDKNFDN-RVLLL-YDGIHYDPLA 231 (307)
T ss_pred cHHHHHHHccccccCceEEeeeehhhhceeEEEEecceeeehhcCCCCCCCc-eEEEE-ecccccChhh
Confidence 47999997665 9999999999999999999999999998988865433233 34455 4599999986
No 4
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=3.3e-06 Score=79.20 Aligned_cols=65 Identities=22% Similarity=0.198 Sum_probs=50.8
Q ss_pred HHHHHcccCCC-CCCCHHHHHHHHHhhCCCEEEEecCCCceeEecCCCCCCCCCEEEEecC-----CCCcccccC
Q 025285 18 VKRFVLTSWMQ-VYGNNVEIQALCEMYNRPIHIYSYTTEPINIFHGSYNTDNPPIRLSYHH-----GNHYNSLVD 86 (255)
Q Consensus 18 fdeYc~rird~-~WGG~iELqALSelynrpI~Vyq~~~~pI~if~~e~~~~~~pI~LSYH~-----GeHYNSV~~ 86 (255)
|++||++++.. .||+.+|+||||.++++|+.++.-.++.|. ++..- .+....+.|++ | |||+..+
T Consensus 236 ~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~~ik-~n~c~--~~~~~e~~~~~Ha~a~G-H~n~~~d 306 (306)
T COG5539 236 WDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASPSIK-CNICG--TGFVGEKDYYAHALATG-HYNFGED 306 (306)
T ss_pred HHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCceEE-eeccc--cccchhhHHHHHHHhhc-CccccCC
Confidence 99999998777 999999999999999999999988776543 32221 23456666766 8 9999853
No 5
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=3.2e-05 Score=74.62 Aligned_cols=71 Identities=17% Similarity=0.173 Sum_probs=53.4
Q ss_pred hHHHHHcc-cCCCCCCCHHHHHHHH---HhhCCCEEEEecCCCceeEecCCCCCCCCCEEEEecCCCCcccccCC
Q 025285 17 VVKRFVLT-SWMQVYGNNVEIQALC---EMYNRPIHIYSYTTEPINIFHGSYNTDNPPIRLSYHHGNHYNSLVDP 87 (255)
Q Consensus 17 ~fdeYc~r-ird~~WGG~iELqALS---elynrpI~Vyq~~~~pI~if~~e~~~~~~pI~LSYH~GeHYNSV~~~ 87 (255)
.|..|.++ .++++||+|+|+||+| +...+|+.+++..........+........+++.|..-.|||.++..
T Consensus 270 ~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 270 DFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKDTCYIQTPPAIEESVKMEKYNFWVEVHYNTARHS 344 (371)
T ss_pred chhhcccccccCCCCcchHHHhhhhhhhhhccccceeecccccceeccCcccccchhhhhhcccchhhhhhcccc
Confidence 48899999 5677999999999999 78889999988876543322233333444577777778999999866
No 6
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=97.49 E-value=0.00022 Score=63.56 Aligned_cols=69 Identities=25% Similarity=0.386 Sum_probs=46.3
Q ss_pred chHHHHHcc-cCCC-CCCCHHHHHHHHHhhCCCEEEEecCCC----ce--eEecCCCCCCCCCEEEEecCCCCccccc
Q 025285 16 FVVKRFVLT-SWMQ-VYGNNVEIQALCEMYNRPIHIYSYTTE----PI--NIFHGSYNTDNPPIRLSYHHGNHYNSLV 85 (255)
Q Consensus 16 y~fdeYc~r-ird~-~WGG~iELqALSelynrpI~Vyq~~~~----pI--~if~~e~~~~~~pI~LSYH~GeHYNSV~ 85 (255)
..+++||++ ++.- .=.+|+.|.|||+++++||.|+-.+.. .+ ..+.+......+.|+|.|--| |||-++
T Consensus 167 ~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~~~~~~~~~~~i~LLyrpg-HYdIly 243 (244)
T PF10275_consen 167 LTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEFPPDNESQEPQITLLYRPG-HYDILY 243 (244)
T ss_dssp S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEES-SSTTSS-SEEEEEETB-EEEEEE
T ss_pred CCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccCCCccCCCCCEEEEEEcCC-cccccc
Confidence 458999988 6664 788999999999999999999987643 11 222222234678999999888 999765
No 7
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=97.25 E-value=0.00048 Score=44.84 Aligned_cols=37 Identities=30% Similarity=0.470 Sum_probs=34.6
Q ss_pred chHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHHH
Q 025285 206 SNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLLE 242 (255)
Q Consensus 206 ~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~e 242 (255)
++.|+.|++|||+..++++|....+-|++.-+.||++
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 5689999999999999999999999999999999974
No 8
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=97.08 E-value=0.001 Score=43.76 Aligned_cols=35 Identities=31% Similarity=0.435 Sum_probs=32.1
Q ss_pred chHHHHHHHhChhHHHHHHHHhhccCChhHHHHHH
Q 025285 206 SNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYL 240 (255)
Q Consensus 206 ~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~ 240 (255)
.+.|+.|+.|||+..++.+|....|-|+|.-+.||
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 56799999999999999999999999999999987
No 9
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=96.70 E-value=0.0026 Score=41.18 Aligned_cols=36 Identities=28% Similarity=0.471 Sum_probs=33.4
Q ss_pred chHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHH
Q 025285 206 SNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLL 241 (255)
Q Consensus 206 ~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~ 241 (255)
++.++.|++|||+..++++|...-|-|++.-+.||+
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 467999999999999999999999999999999984
No 10
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.08 E-value=0.0092 Score=55.11 Aligned_cols=76 Identities=25% Similarity=0.362 Sum_probs=54.4
Q ss_pred ccCCC-Ccch-----HHHHHcc-cCCC-CCCCHHHHHHHHHhhCCCEEEEecCCCce-eEecCCCC-CCCCCEEEEecCC
Q 025285 9 CNCDS-HSFV-----VKRFVLT-SWMQ-VYGNNVEIQALCEMYNRPIHIYSYTTEPI-NIFHGSYN-TDNPPIRLSYHHG 78 (255)
Q Consensus 9 ~n~Df-~~y~-----fdeYc~r-ird~-~WGG~iELqALSelynrpI~Vyq~~~~pI-~if~~e~~-~~~~pI~LSYH~G 78 (255)
.|+|| .+|+ .+.||.+ ++.- .=-|||+|-|||+.+++.|.|--.+...- .++|-.+. ...|.|.|.|-.|
T Consensus 169 ~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fpe~s~P~I~LLYrpG 248 (256)
T KOG3991|consen 169 SNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFPEASAPEIYLLYRPG 248 (256)
T ss_pred hChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCccccCceEEEEecCC
Confidence 56776 6664 8999999 5443 55799999999999999998876543211 22222232 3567899998866
Q ss_pred CCccccc
Q 025285 79 NHYNSLV 85 (255)
Q Consensus 79 eHYNSV~ 85 (255)
|||-++
T Consensus 249 -HYdilY 254 (256)
T KOG3991|consen 249 -HYDILY 254 (256)
T ss_pred -cccccc
Confidence 999887
No 11
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=93.28 E-value=0.012 Score=55.70 Aligned_cols=65 Identities=14% Similarity=0.212 Sum_probs=48.3
Q ss_pred HHHHHcccCCC-CCC-CHHHHHHHHHhhCCCEEEEecCCCceeEecCCCCCCCCCEEEEecCCCCccccc
Q 025285 18 VKRFVLTSWMQ-VYG-NNVEIQALCEMYNRPIHIYSYTTEPINIFHGSYNTDNPPIRLSYHHGNHYNSLV 85 (255)
Q Consensus 18 fdeYc~rird~-~WG-G~iELqALSelynrpI~Vyq~~~~pI~if~~e~~~~~~pI~LSYH~GeHYNSV~ 85 (255)
--.||.+++.. .|| |++|+-+||..+++.|.|.......+..|++.- -...+++.|- |.||+...
T Consensus 164 ~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~--~~q~~~i~f~-g~hfD~~t 230 (306)
T COG5539 164 VIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHP--YVQRISILFT-GIHFDEET 230 (306)
T ss_pred hHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCCh--hhhhhhhhhc-ccccchhh
Confidence 55899998776 999 999999999999999999988765544442211 1123555554 88999875
No 12
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.14 E-value=0.63 Score=45.31 Aligned_cols=42 Identities=21% Similarity=0.317 Sum_probs=37.9
Q ss_pred cCCcccchHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHH
Q 025285 200 LSDTVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLL 241 (255)
Q Consensus 200 ~~~~~~~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~ 241 (255)
..++.+..+|+.+++|||.-.+|..|-..==-|||.-|-||+
T Consensus 151 ~~g~~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~ 192 (378)
T TIGR00601 151 VVGSERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLL 192 (378)
T ss_pred ccchHHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHH
Confidence 356788999999999999999999998877789999999998
No 13
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=88.48 E-value=1 Score=43.63 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=37.9
Q ss_pred ccCCcccchHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHH
Q 025285 199 ELSDTVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLL 241 (255)
Q Consensus 199 ~~~~~~~~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~ 241 (255)
...++.++++|+.++.||+.-.+|+-|---==-+||.-|-|||
T Consensus 129 Lv~G~~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl 171 (340)
T KOG0011|consen 129 LVVGSEYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLL 171 (340)
T ss_pred hhccchhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHh
Confidence 3456789999999999999999999987776789999999998
No 14
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.10 E-value=0.81 Score=44.55 Aligned_cols=43 Identities=21% Similarity=0.319 Sum_probs=39.3
Q ss_pred CcccchHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHHHhC
Q 025285 202 DTVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLLETG 244 (255)
Q Consensus 202 ~~~~~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~e~~ 244 (255)
.+....+|+.|.+|||.-.+|||||---..|-+.-.|||+|-+
T Consensus 334 T~eE~~AIeRL~~LGF~r~~viqaY~ACdKNEelAAn~Lf~~~ 376 (378)
T TIGR00601 334 TPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQN 376 (378)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHhhc
Confidence 3557789999999999999999999999999999999999854
No 15
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=83.84 E-value=1.1 Score=33.03 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=20.2
Q ss_pred cchHHHHHHHhChhHHHHHHHHhhcc
Q 025285 205 LSNSMQMVLSMGFSYLQVIEAYSIFG 230 (255)
Q Consensus 205 ~~~~~~~~~~mgf~~~~~~~ay~i~g 230 (255)
...-|..+++|||+.+.||+|.--.|
T Consensus 9 ~~~lVd~F~~mGF~~dkVvevlrrlg 34 (55)
T PF09288_consen 9 DKDLVDQFENMGFERDKVVEVLRRLG 34 (55)
T ss_dssp SHHHHHHHHHHT--HHHHHHHHHHS-
T ss_pred CHHHHHHHHHcCCcHHHHHHHHHHhC
Confidence 35678999999999999999998777
No 16
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=66.29 E-value=11 Score=38.62 Aligned_cols=45 Identities=22% Similarity=0.208 Sum_probs=40.0
Q ss_pred CCcccchHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHHHhCC
Q 025285 201 SDTVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLLETGS 245 (255)
Q Consensus 201 ~~~~~~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~e~~~ 245 (255)
|..+...++..||+|||+-.-+--|-.-||-++|..+-.|+=.+.
T Consensus 425 p~~vd~~~la~Lv~mGF~e~~A~~ALe~~gnn~~~a~~~L~~s~~ 469 (568)
T KOG2561|consen 425 PEQVDGISLAELVSMGFEEGKARSALEAGGNNEDTAQRLLSASVA 469 (568)
T ss_pred CcccchhhHHHHHHhccccchHHHHHHhcCCcHHHHHHHHHHhCC
Confidence 445788999999999999999999999999999999999986643
No 17
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=60.69 E-value=12 Score=36.50 Aligned_cols=43 Identities=21% Similarity=0.330 Sum_probs=38.5
Q ss_pred CcccchHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHHHhC
Q 025285 202 DTVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLLETG 244 (255)
Q Consensus 202 ~~~~~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~e~~ 244 (255)
.+.-.++|..|-+|||.-..|||||----.|=.+-.|||++-.
T Consensus 295 tpee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~ 337 (340)
T KOG0011|consen 295 TPEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHS 337 (340)
T ss_pred CHHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhc
Confidence 3567789999999999999999999888889999999999854
No 18
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=57.01 E-value=14 Score=38.48 Aligned_cols=38 Identities=24% Similarity=0.468 Sum_probs=34.1
Q ss_pred chHHHHHHHhChhHHHHHHHHhhccC-ChhHHHHHHHHh
Q 025285 206 SNSMQMVLSMGFSYLQVIEAYSIFGD-DVDSMVCYLLET 243 (255)
Q Consensus 206 ~~~~~~~~~mgf~~~~~~~ay~i~gd-~~d~~~~~~~e~ 243 (255)
-++|+.|+.|||+.-+...|--|+|. |..+..|||.|-
T Consensus 559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqH 597 (749)
T COG5207 559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQH 597 (749)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhh
Confidence 46799999999999999999999997 888888888875
No 19
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=52.76 E-value=3.2 Score=40.61 Aligned_cols=41 Identities=15% Similarity=-0.040 Sum_probs=36.8
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHhhhch
Q 025285 121 QQIDNALLAEGRFYSDLELTEKEIECMVMEVSRAEYLAGDN 161 (255)
Q Consensus 121 ~~ie~~ml~dk~~~tD~e~t~~eie~~v~~~s~~~~l~~~~ 161 (255)
.++++.|+.+++..|||..|...|++++.+++|..|++...
T Consensus 298 ~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~n~~~~~h~ 338 (371)
T KOG2605|consen 298 EEIEKPLNITSFKDTCYIQTPPAIEESVKMEKYNFWVEVHY 338 (371)
T ss_pred hhccccceeecccccceeccCcccccchhhhhhcccchhhh
Confidence 46777888999999999999999999999999999998753
No 20
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=41.89 E-value=23 Score=37.70 Aligned_cols=39 Identities=31% Similarity=0.442 Sum_probs=34.7
Q ss_pred cccchHHHHHHHhChhHHHHHHHHhhccCChhHHHHHHH
Q 025285 203 TVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLL 241 (255)
Q Consensus 203 ~~~~~~~~~~~~mgf~~~~~~~ay~i~gd~~d~~~~~~~ 241 (255)
.+.+.+++++++|||+-.|++.|-..---++...+-||.
T Consensus 633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDWif 671 (763)
T KOG0944|consen 633 EVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDWIF 671 (763)
T ss_pred CCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHHHH
Confidence 467789999999999999999999998888888888875
No 21
>PF05801 DUF840: Lagovirus protein of unknown function (DUF840); InterPro: IPR008558 This family consists of several Lagovirus sequences of unknown function, largely from Oryctolagus cuniculus hemorrhagic disease virus.
Probab=36.69 E-value=50 Score=27.21 Aligned_cols=34 Identities=24% Similarity=0.400 Sum_probs=25.9
Q ss_pred cCCCCCCCCCCcccHHHHHHHHHHhHHHHHHHHHHhcCccc
Q 025285 94 AGLGFSCLRGTNVDKDQVKAAIKAQQDQQIDNALLAEGRFY 134 (255)
Q Consensus 94 ~gLglp~~~p~~ad~~~~~~Ai~~se~~~ie~~ml~dk~~~ 134 (255)
+||||.+ -.-+..|+-.+++.+++++-||.++..
T Consensus 5 igl~lag-------a~vlsnallrrqelqlqkqalenglvl 38 (114)
T PF05801_consen 5 IGLGLAG-------ASVLSNALLRRQELQLQKQALENGLVL 38 (114)
T ss_pred hccccch-------HHHHHHHHHHHHHHHHHHHHHhcCeee
Confidence 4677655 456777888889999999999887743
No 22
>PF05697 Trigger_N: Bacterial trigger factor protein (TF); InterPro: IPR008881 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This group of sequences contain the ribosomal subunit association domain.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 2D3O_1 1W26_A 1P9Y_A 1OMS_C 1T11_A 3GU0_A 2NSB_A 2NSC_A 3GTY_X.
Probab=35.28 E-value=85 Score=25.68 Aligned_cols=45 Identities=7% Similarity=0.116 Sum_probs=27.1
Q ss_pred CCCCCCCCCCcccHHHHHHHHHHhHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHhhhc
Q 025285 95 GLGFSCLRGTNVDKDQVKAAIKAQQDQQIDNALLAEGRFYSDLELTEKEIECMVMEVSRAEYLAGD 160 (255)
Q Consensus 95 gLglp~~~p~~ad~~~~~~Ai~~se~~~ie~~ml~dk~~~tD~e~t~~eie~~v~~~s~~~~l~~~ 160 (255)
-..+|||+||.|-...+++-+..+ -.++.-+.++++++.+++++.
T Consensus 38 ~~~ipGFRkGK~P~~vi~~~~g~~---------------------i~~~~~~~~~~~~~~~~~~~~ 82 (145)
T PF05697_consen 38 KVKIPGFRKGKAPRNVIEKRYGKE---------------------IREEAIEELLQEAYEEAIKEE 82 (145)
T ss_dssp TTTBTTS-TTSS-HHHHHHHHCHH---------------------HHHHHHHHHHHHHHHHHHHHT
T ss_pred hCCCCCCCCCCCCHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHHHHc
Confidence 357999999999887655443321 123334556677777777763
No 23
>PTZ00250 variable surface protein Vir23; Provisional
Probab=28.47 E-value=33 Score=33.42 Aligned_cols=18 Identities=39% Similarity=0.787 Sum_probs=15.4
Q ss_pred HhhccCChhHHHHHHHHh
Q 025285 226 YSIFGDDVDSMVCYLLET 243 (255)
Q Consensus 226 y~i~gd~~d~~~~~~~e~ 243 (255)
+-|||+|||.+++.|+-+
T Consensus 264 ~~~~~~~~~~~~~~~~~~ 281 (350)
T PTZ00250 264 LPIFGNDADDIINILLKV 281 (350)
T ss_pred eeecCCCHHHHHHHHHhh
Confidence 458999999999988765
No 24
>KOG1252 consensus Cystathionine beta-synthase and related enzymes [Amino acid transport and metabolism]
Probab=28.20 E-value=1.1e+02 Score=30.38 Aligned_cols=107 Identities=20% Similarity=0.211 Sum_probs=59.3
Q ss_pred CcchHHHHHcccCC--C--CCCCHHHHHHHHHhhCCCEEEEecCCCceeEecCCCC-CCCCCEEEEecCCCCcccccCCC
Q 025285 14 HSFVVKRFVLTSWM--Q--VYGNNVEIQALCEMYNRPIHIYSYTTEPINIFHGSYN-TDNPPIRLSYHHGNHYNSLVDPR 88 (255)
Q Consensus 14 ~~y~fdeYc~rird--~--~WGG~iELqALSelynrpI~Vyq~~~~pI~if~~e~~-~~~~pI~LSYH~GeHYNSV~~~~ 88 (255)
..|.+++|++--.. + +=| .||.-=. .=++.|.|+-.++.--...=+.|- ..++++.+. --..+|.++.++.
T Consensus 181 na~~l~Qf~np~Np~~hy~ttg--~EI~~q~-~g~vDi~V~gaGTGGTitgvGRylke~~~~~kVv-~vdp~~S~~~~~~ 256 (362)
T KOG1252|consen 181 NAYILDQFHNPGNPLAHYETTG--PEIWRQL-DGKVDIFVAGAGTGGTITGVGRYLKEQNPNIKVV-GVDPQESIVLSGG 256 (362)
T ss_pred ChHHHHHhcCCCCccccccccc--HHHHHHh-cCCCCEEEeccCCCceeechhHHHHHhCCCCEEE-EeCCCcceeccCC
Confidence 45667888775211 1 223 2332222 556777888776532111111221 123334332 2245666666544
Q ss_pred CCCC------ccCCCCCCCCCCcccHHHHHHHHHHhHHHHHHHHH
Q 025285 89 RMTV------GAGLGFSCLRGTNVDKDQVKAAIKAQQDQQIDNAL 127 (255)
Q Consensus 89 ~pti------G~gLglp~~~p~~ad~~~~~~Ai~~se~~~ie~~m 127 (255)
.+.. |+|-| |.|+..|.+.|.+.++.+.++-++-||
T Consensus 257 ~~g~~~~~I~GIGyg---~~p~~ld~~~vd~~~~~~~d~A~~~Ar 298 (362)
T KOG1252|consen 257 KPGPTFHKIQGIGYG---FIPTTLDTKLVDEVLKVSSDEAIEMAR 298 (362)
T ss_pred CCCCCccceeccccC---cCccccchHHHHHHHHhCCHHHHHHHH
Confidence 4432 55555 799999999999999988777777665
No 25
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=25.88 E-value=1.7e+02 Score=23.62 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=37.7
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHHhcCccccchHHHHHHHHHHHHHH
Q 025285 105 NVDKDQVKAAIKAQQDQQIDNALLAEGRFYSDLELTEKEIECMVMEV 151 (255)
Q Consensus 105 ~ad~~~~~~Ai~~se~~~ie~~ml~dk~~~tD~e~t~~eie~~v~~~ 151 (255)
.++.++...++=..+..++|+-.-+.-+...+++...+||++..+.+
T Consensus 30 ~~~~~~~n~~iyr~qL~ELe~d~~~G~l~~~e~~~~~~El~rrLL~d 76 (117)
T TIGR03142 30 TVDRDELNLAVYRDRLAELERDLAEGLLDEAEAEAARAELQRRLLAD 76 (117)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHC
Confidence 36677888889888888999988777777788888888888877644
No 26
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=21.82 E-value=1.7e+02 Score=31.52 Aligned_cols=39 Identities=18% Similarity=0.268 Sum_probs=33.9
Q ss_pred cchHHHHHHHhChhHHHHHHHHhhcc-CChhHHHHHHHHh
Q 025285 205 LSNSMQMVLSMGFSYLQVIEAYSIFG-DDVDSMVCYLLET 243 (255)
Q Consensus 205 ~~~~~~~~~~mgf~~~~~~~ay~i~g-d~~d~~~~~~~e~ 243 (255)
..+.|..|+.|||+....-.|.-++| ++...--|||+|-
T Consensus 571 d~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~H 610 (763)
T KOG0944|consen 571 DRSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEH 610 (763)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHh
Confidence 44678899999999999999999996 6788888999886
No 27
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=21.57 E-value=2.5e+02 Score=18.48 Aligned_cols=37 Identities=19% Similarity=0.193 Sum_probs=22.8
Q ss_pred hHHHHHHHh--ChhHHHHHHHHhhccCChhHHHHHHHHh
Q 025285 207 NSMQMVLSM--GFSYLQVIEAYSIFGDDVDSMVCYLLET 243 (255)
Q Consensus 207 ~~~~~~~~m--gf~~~~~~~ay~i~gd~~d~~~~~~~e~ 243 (255)
+.|+.|.+| .++...+..+..-.+.++|.-+..|+|.
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 345555555 4555556666666777777777777763
No 28
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=21.33 E-value=1.3e+02 Score=20.63 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=19.5
Q ss_pred ccchHHHHHHHhChhHHHHHHHHhhc
Q 025285 204 VLSNSMQMVLSMGFSYLQVIEAYSIF 229 (255)
Q Consensus 204 ~~~~~~~~~~~mgf~~~~~~~ay~i~ 229 (255)
..++.+.-|++.||+-.++-.|-.=.
T Consensus 2 ~~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 2 ALEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 35678899999999988887776544
Done!