Query 045299
Match_columns 574
No_of_seqs 205 out of 571
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 11:49:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045299.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045299hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00463 SMR Small MutS-rela 99.6 4.4E-15 9.6E-20 124.3 8.7 78 490-574 2-80 (80)
2 PF08590 DUF1771: Domain of un 99.5 1.1E-15 2.5E-20 125.0 1.1 66 413-478 1-66 (66)
3 PF01713 Smr: Smr domain; Int 99.5 3.3E-14 7.1E-19 119.8 7.2 71 492-573 1-82 (83)
4 KOG2401 Predicted MutS-related 99.0 1.8E-09 4E-14 117.1 11.3 410 107-564 15-429 (448)
5 COG2840 Uncharacterized protei 98.8 1.5E-08 3.3E-13 98.8 8.8 77 488-573 95-178 (184)
6 PRK04946 hypothetical protein; 98.4 1E-06 2.2E-11 85.9 8.0 73 487-573 93-172 (181)
7 PRK00409 recombination and DNA 97.7 0.00011 2.3E-09 85.6 8.4 72 488-573 703-781 (782)
8 TIGR01069 mutS2 MutS2 family p 97.5 0.00021 4.5E-09 83.1 8.3 71 489-573 693-770 (771)
9 PF07145 PAM2: Ataxin-2 C-term 97.5 5.2E-05 1.1E-09 48.3 1.3 16 20-35 2-17 (18)
10 PF02845 CUE: CUE domain; Int 96.0 0.012 2.5E-07 44.3 4.4 36 223-258 5-40 (42)
11 smart00546 CUE Domain that may 94.3 0.065 1.4E-06 40.4 4.0 35 223-257 6-40 (43)
12 PF03474 DMA: DMRTA motif; In 90.7 0.42 9E-06 36.4 4.0 37 220-256 2-38 (39)
13 COG1193 Mismatch repair ATPase 89.6 0.69 1.5E-05 54.5 6.7 71 489-573 676-753 (753)
14 PF01963 TraB: TraB family; I 71.9 15 0.00032 36.5 7.6 89 426-563 170-258 (259)
15 KOG2401 Predicted MutS-related 70.3 1.8 4E-05 47.7 0.8 136 411-561 240-375 (448)
16 PF00627 UBA: UBA/TS-N domain; 67.8 8.8 0.00019 28.0 3.8 32 223-256 6-37 (37)
17 PLN03218 maturation of RBCL 1; 63.8 13 0.00029 45.7 6.4 81 488-572 920-1011(1060)
18 PRK06369 nac nascent polypepti 61.4 7.1 0.00015 36.2 2.7 37 219-257 77-113 (115)
19 TIGR00264 alpha-NAC-related pr 59.7 9 0.0002 35.7 3.1 37 219-257 79-115 (116)
20 cd00291 SirA_YedF_YeeD SirA, Y 59.1 36 0.00078 27.2 6.2 65 491-573 1-67 (69)
21 smart00165 UBA Ubiquitin assoc 59.0 14 0.0003 26.5 3.4 25 232-256 12-36 (37)
22 cd00194 UBA Ubiquitin Associat 58.6 15 0.00032 26.5 3.5 26 232-257 12-37 (38)
23 cd03420 SirA_RHOD_Pry_redox Si 55.6 39 0.00085 27.8 6.0 65 491-573 1-67 (69)
24 smart00685 DM14 Repeats in fly 53.7 61 0.0013 26.9 6.6 39 425-463 4-43 (59)
25 PF01206 TusA: Sulfurtransfera 53.0 25 0.00054 28.5 4.4 65 491-573 2-68 (70)
26 PF04505 Dispanin: Interferon- 51.2 18 0.00039 31.3 3.4 27 433-459 42-68 (82)
27 PF14346 DUF4398: Domain of un 49.1 1.2E+02 0.0027 26.6 8.4 44 424-467 41-84 (103)
28 PF10862 FcoT: FcoT-like thioe 48.4 2.6 5.6E-05 40.9 -2.4 19 81-99 86-104 (157)
29 TIGR01689 EcbF-BcbF capsule bi 43.7 42 0.0009 31.3 4.8 37 524-563 41-82 (126)
30 COG1308 EGD2 Transcription fac 42.9 23 0.00051 33.3 3.0 37 219-257 85-121 (122)
31 PF03357 Snf7: Snf7; InterPro 41.0 1.7E+02 0.0036 27.2 8.5 57 413-469 9-65 (171)
32 cd03423 SirA SirA (also known 39.2 84 0.0018 25.8 5.5 64 492-573 2-67 (69)
33 PF13763 DUF4167: Domain of un 37.4 1.3E+02 0.0028 26.5 6.5 38 430-467 41-78 (80)
34 PRK00299 sulfur transfer prote 36.7 1.3E+02 0.0027 25.8 6.3 68 488-573 8-77 (81)
35 cd03421 SirA_like_N SirA_like_ 35.8 1.5E+02 0.0032 23.9 6.3 64 491-573 1-65 (67)
36 PRK11018 hypothetical protein; 30.6 1.9E+02 0.0041 24.5 6.4 68 488-573 7-76 (78)
37 PF10006 DUF2249: Uncharacteri 29.6 1.5E+02 0.0033 24.2 5.5 63 491-573 1-67 (69)
38 PF02403 Seryl_tRNA_N: Seryl-t 27.9 3.1E+02 0.0066 24.1 7.6 59 409-469 33-91 (108)
39 PRK06851 hypothetical protein; 27.6 5.2E+02 0.011 28.5 10.6 128 413-561 116-245 (367)
40 COG2250 Uncharacterized conser 24.7 2.6E+02 0.0056 26.2 6.7 39 417-455 2-40 (132)
41 PLN03086 PRLI-interacting fact 23.8 5.3E+02 0.011 30.2 10.2 55 499-559 55-109 (567)
42 PF09507 CDC27: DNA polymerase 22.8 1.1E+02 0.0023 32.9 4.4 40 496-537 13-52 (430)
43 cd05126 Mth938 Mth938 domain. 22.1 78 0.0017 29.2 2.7 50 493-563 42-91 (117)
44 COG2023 RPR2 RNase P subunit R 21.6 2.8E+02 0.006 25.7 6.0 40 422-462 8-47 (105)
45 TIGR00823 EIIA-LAC phosphotran 20.9 3.1E+02 0.0067 24.7 6.2 67 425-504 15-81 (99)
No 1
>smart00463 SMR Small MutS-related domain.
Probab=99.59 E-value=4.4e-15 Score=124.26 Aligned_cols=78 Identities=31% Similarity=0.462 Sum_probs=69.3
Q ss_pred eeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCcccc-CCCcE
Q 045299 490 RMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYTE-PQPGL 568 (574)
Q Consensus 490 ~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~E-~n~G~ 568 (574)
++|||||+++.||+.+|+.+|..++.. +....+.||||+|+||.+|+ ++|+++|.++|. ..+|.|.+ .+.|+
T Consensus 2 ~~lDLHG~~~~eA~~~l~~~l~~~~~~----~~~~~~~II~G~G~~s~~g~--~~i~~~l~~~l~-~~~~~~~~~~~~G~ 74 (80)
T smart00463 2 WSLDLHGLTVEEALTALDKFLNNARLK----GLEQKLVIITGKGKHSLGGK--SGVKPALKEHLR-VESFRFAEEGNSGV 74 (80)
T ss_pred CeEEcCCCCHHHHHHHHHHHHHHHHHc----CCCceEEEEEcccCCCccch--hhHHHHHHhchh-hcccccCCCCCCeE
Confidence 689999999999999999999997642 22158999999999999887 999999999999 99999987 69999
Q ss_pred EEEEEC
Q 045299 569 LRVVIY 574 (574)
Q Consensus 569 L~V~L~ 574 (574)
++|.|+
T Consensus 75 ~~v~l~ 80 (80)
T smart00463 75 LVVKLK 80 (80)
T ss_pred EEEEeC
Confidence 999873
No 2
>PF08590 DUF1771: Domain of unknown function (DUF1771); InterPro: IPR013899 This domain is almost always found adjacent to IPR002625 from INTERPRO. ; PDB: 2VKC_A.
Probab=99.54 E-value=1.1e-15 Score=124.99 Aligned_cols=66 Identities=50% Similarity=0.726 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 045299 413 MYSELREEARDHARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRNP 478 (574)
Q Consensus 413 ~Y~e~R~eA~~~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAAeaIf~~RN~ 478 (574)
+|.++|.+|.+|++.|++||++|++||++||+++|++||++|+.|+++|+++|.+||+.||..||.
T Consensus 1 ~Y~~~R~~A~~~~~~r~~~~~~A~~Ay~~Gd~~~A~~ls~~gk~~~~~~~~~n~~AA~~I~~~~N~ 66 (66)
T PF08590_consen 1 DYEKLRAEADEHARKRNECFQKAAEAYRRGDKAAAKELSEEGKQHNEKMKEANRQAAEAIFEERNA 66 (66)
T ss_dssp --------------------------------------------------SHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 589999999999999999999999999999999999999999999999999999999999999973
No 3
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=99.51 E-value=3.3e-14 Score=119.80 Aligned_cols=71 Identities=39% Similarity=0.589 Sum_probs=57.1
Q ss_pred eecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccccC-------
Q 045299 492 IDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYTEP------- 564 (574)
Q Consensus 492 IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~E~------- 564 (574)
|||||++++||+.+|+++|..++.. ....++||||+|+||.+| .||++|.+||. + ++.+.++
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~-----~~~~~~II~G~G~hS~~g----~Lk~~V~~~L~-~-~~~~~~v~~~~~~~ 69 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQR-----GIRELRIITGKGNHSKGG----VLKRAVRRWLE-E-GYQYEEVLAYRDAE 69 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHT-----THSEEEEE--STCTCCTS----HHHHHHHHHHH-H-THCCTTEEEEEE--
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHc-----CCCEEEEEeccCCCCCCC----cHHHHHHHHHH-h-hhccchhheeeecC
Confidence 8999999999999999999987632 237899999999999988 39999999998 6 7666442
Q ss_pred ----CCcEEEEEE
Q 045299 565 ----QPGLLRVVI 573 (574)
Q Consensus 565 ----n~G~L~V~L 573 (574)
++|+++|.|
T Consensus 70 ~~~g~~G~~~V~l 82 (83)
T PF01713_consen 70 PEDGNSGATIVYL 82 (83)
T ss_dssp CCCTGGGEEEEEE
T ss_pred CCCCCCeEEEEEe
Confidence 899999986
No 4
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=99.00 E-value=1.8e-09 Score=117.08 Aligned_cols=410 Identities=20% Similarity=0.163 Sum_probs=285.1
Q ss_pred CCcccccccccCCCCCCCccCCCCCCCcccccccccCccccCCCchhhhhcccCCcCCCCCCccccCCCCCCcccccccC
Q 045299 107 LGGLSLAGLSLHDGIEGSRFPASTGSGYVLSEQQELSPHHINGNSFAEKMRFSASSYGEDPTAANFLNLSPRPWDKQILG 186 (574)
Q Consensus 107 ~~~lsl~gls~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (574)
-..+++++.+.....+...+.....+ +.++.+-.++.+.....+.++..+|+......+++.-.+.+...+.|+.++..
T Consensus 15 s~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~ 93 (448)
T KOG2401|consen 15 SLTLSLAAFSFSFKLVDLKAASEESS-DEVDLGPPELSEMATSTSSADRLQYTIELLEPSPSSVSFESLRARASDENVDR 93 (448)
T ss_pred cchhccchhhhhhhhHhhhhcccccc-cccccCCCcchhhccccchhhhhcccccccCCCcccccccccccchhhhcccc
Confidence 34577788777776666555555554 56666777777777788888999999999999999999999999999988777
Q ss_pred cccc----ccCCCCCCCCCCcccccccccccccccCCCCchhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHHHhhhhh
Q 045299 187 SDQL----REGHPYNGNSRHGFVNDMTGEIGMIEDTEMNPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLTQLELQ 262 (574)
Q Consensus 187 ~~~~----~~~~~~~~~s~~g~~~~~~~~~~~~~~~~~dplefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L~~lE~~ 262 (574)
+-+. |-...-.+...+.+....+.+.- -.....|..+|.-.++++..+...+.+..+++...-.|++++++..+
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~e~~~~~~~f~~~~~~~~~~~~~~~~~~~ 171 (448)
T KOG2401|consen 94 GNQERILDRSRNQVAGKLKVSFVEKKLNEEE--PQKEINPDGRILPEDPSFEESFRVENGFDPGEAIAFKIEDLPQKQVE 171 (448)
T ss_pred HHHHhhcccccccccccccccccccccCccc--cccccCCcccccccccchHHHHHHhccCccchhhhcchhhhcccccc
Confidence 6665 55566667778888877777664 33445567888889999999999999999999999999999999988
Q ss_pred hcCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCcccccccccccCCCCCcchhhhhhhhcCCCCCCCCCCcchHHHH
Q 045299 263 VDGGFNQNPHSKPLSSPNLSAMDFPVLTVPDGQTGSQKYAVDDLQQTGNPFRSADKENLLMFKTSSSFPSRGATDFASAV 342 (574)
Q Consensus 263 ~d~~~~q~~~~~~~~~p~~~~~dFPsl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~d~~Sav 342 (574)
.+...|.... ||.+.....-....++-++.+.+..+......++.-++++..-+.......+..+++
T Consensus 172 ~~~~~n~~~~-------------~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (448)
T KOG2401|consen 172 GEDVDNCKVK-------------NQITNSSDSKMATEPGLNDSLKKAYENVDSSEESVELLRKEGFSVDVPSNAEKNSAK 238 (448)
T ss_pred ccccccceee-------------ccccccccccccccccccchhhccccccCcchhhhhhhccCCCCccCcchhhccccc
Confidence 6534322222 455555555555556667778888888888888766666653333333456677778
Q ss_pred HHhhhcccccccccccCCCCCCCCCCCCcccccccccCCCCCCccccccccCCCCCCCCcccccchhhHHHHHHHHHHHH
Q 045299 343 RKLASQDSGAWKYERNGSADSTIGSSRSSNVSASAYNSGHGRGIYADRLQNRGSARTAPVWLETGEAVANMYSELREEAR 422 (574)
Q Consensus 343 ~elasq~s~~~k~~~~~~~~~~~g~~r~~~~~~~~~~~~~~~~~~~~~~q~~~s~~~~p~wl~Tg~a~~~~Y~e~R~eA~ 422 (574)
+....+.+..+++.......-.....|. +......-.+-.................|-+.......++.....+..
T Consensus 239 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~s~~~~~~~ 314 (448)
T KOG2401|consen 239 RLEELQKSQPEEDKAKKLRDQLYKSKRP----AGSGKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNKESIKSEREI 314 (448)
T ss_pred chhhcchhhhccchhhhHHHhhhhhccc----ccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhhhhhhhhHHh
Confidence 8888888888877655444333333322 111100000001011111111112223444555555666666677777
Q ss_pred HHHH-HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcccCCCCCCceeeecCCCCHHH
Q 045299 423 DHAR-LRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRNPVELQGNGRGQDRMIDLHGLHVSE 501 (574)
Q Consensus 423 ~~a~-~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAAeaIf~~RN~~~~qG~g~~~~~~IDLHGLhV~E 501 (574)
+..+ .+..+.++++..+..+....|.++.-.+......+.+....+-+.+...++... ......++|+-.+.+
T Consensus 315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~------~r~~~~~~~~~~i~~ 388 (448)
T KOG2401|consen 315 DNQRLYKKAAEQKAQPEIEDAINLQASELKPKVSLAVKGSYAVAKLKPATQWKLDNEEI------ERRSEVGEHGEKISE 388 (448)
T ss_pred hhhhHHHHHHHhhhhhhhhhhhhhhhhhhchhhhhcccccchhhhcchHHHHHHhhhhh------hcccccccchhhhHh
Confidence 7776 888999999999999999999999999888888888887777777777776655 346677777777766
Q ss_pred HHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccccC
Q 045299 502 AIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYTEP 564 (574)
Q Consensus 502 Av~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~E~ 564 (574)
+...+ .+.+++|+|.||.+. +++..++.+.+. ..++.+.+.
T Consensus 389 ~~~~~------------------~~qv~~~~~~~s~~~---~~~~~~~~~~~~-~~~~~~~~~ 429 (448)
T KOG2401|consen 389 LSRRL------------------KLQVLFGRGIHSRGE---ARLPRAEKRSYE-DPPQGFVEE 429 (448)
T ss_pred Hhhhc------------------cccccccccccCccc---hhhhhhhhhhcc-CCccceeee
Confidence 55433 355688999999987 688888888777 778877543
No 5
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.80 E-value=1.5e-08 Score=98.77 Aligned_cols=77 Identities=29% Similarity=0.420 Sum_probs=63.6
Q ss_pred CceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCC--CccccC-
Q 045299 488 QDRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEG--LDYTEP- 564 (574)
Q Consensus 488 ~~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g--~~f~E~- 564 (574)
.+..||||||+++||-..|..+|..++. . ...++.||||+|. |.|+. +.||..|..||. .+- ..|.+.
T Consensus 95 ~e~~LDLHG~tq~eAr~~L~~Fi~~a~~----~-~~rcv~VihGkG~-s~g~~--~vLK~~Vp~WL~-qhp~V~a~~~a~ 165 (184)
T COG2840 95 PEARLDLHGLTQEEARQELGAFIARARA----E-GLRCVLVIHGKGR-SKGSK--PVLKSQVPRWLT-QHPDVLAFHQAP 165 (184)
T ss_pred cceeeeccCCCHHHHHHHHHHHHHHHHH----h-CCcEEEEEeCCCc-CCCCc--hhHHHHHHHHHH-hChHHHhhcccc
Confidence 6889999999999999999999988653 2 2478999999999 99987 999999999999 532 234432
Q ss_pred ----CCcEEEEEE
Q 045299 565 ----QPGLLRVVI 573 (574)
Q Consensus 565 ----n~G~L~V~L 573 (574)
..|.|+|.|
T Consensus 166 ~~hGG~GAlyVlL 178 (184)
T COG2840 166 RRHGGDGALYVLL 178 (184)
T ss_pred hhcCCceEEEEEE
Confidence 478898876
No 6
>PRK04946 hypothetical protein; Provisional
Probab=98.37 E-value=1e-06 Score=85.94 Aligned_cols=73 Identities=21% Similarity=0.226 Sum_probs=58.8
Q ss_pred CCceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCC--ccc--
Q 045299 487 GQDRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGL--DYT-- 562 (574)
Q Consensus 487 ~~~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~--~f~-- 562 (574)
..+..|||||++++||...|..+|..+.. .+ ..++.||+|+|. ++||.+|..||. ++.+ .|.
T Consensus 93 ~~~~~LDLhG~~~eeA~~~L~~fl~~a~~----~g-~r~v~IIHGkG~--------gvLk~~V~~wL~-q~~~V~af~~A 158 (181)
T PRK04946 93 SPELFLDLHGLTQLQAKQELGALIAACRK----EH-VFCACVMHGHGK--------HILKQQTPLWLA-QHPDVMAFHQA 158 (181)
T ss_pred CCceEEECCCCCHHHHHHHHHHHHHHHHH----cC-CCEEEEEcCCCH--------hHHHHHHHHHHc-CCchhheeecc
Confidence 46789999999999999999999988642 23 468999999984 489999999998 5542 353
Q ss_pred ---cCCCcEEEEEE
Q 045299 563 ---EPQPGLLRVVI 573 (574)
Q Consensus 563 ---E~n~G~L~V~L 573 (574)
+-+.|+++|.|
T Consensus 159 ~~~~GG~GA~~VlL 172 (181)
T PRK04946 159 PKEWGGDAALLVLI 172 (181)
T ss_pred CcccCCceEEEEEE
Confidence 23589999987
No 7
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=97.66 E-value=0.00011 Score=85.62 Aligned_cols=72 Identities=28% Similarity=0.305 Sum_probs=57.2
Q ss_pred CceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCc--c----
Q 045299 488 QDRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLD--Y---- 561 (574)
Q Consensus 488 ~~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~--f---- 561 (574)
....|||||++++||+..|+.+|.... ..| ...++||+|+|. ..|+.+|..||. ++.+- |
T Consensus 703 ~~~~lDL~G~~~eeA~~~l~~fl~~a~----~~g-~~~v~IIHGkGt--------G~Lr~~v~~~L~-~~~~V~~f~~a~ 768 (782)
T PRK00409 703 VSLELDLRGMRYEEALERLDKYLDDAL----LAG-YGEVLIIHGKGT--------GKLRKGVQEFLK-KHPSVKSFRDAP 768 (782)
T ss_pred CCceEECCCCCHHHHHHHHHHHHHHHH----HcC-CCEEEEEcCCCh--------hHHHHHHHHHHc-CCCceeeeeecC
Confidence 356899999999999999999998853 233 478999999983 489999999999 66532 3
Q ss_pred -ccCCCcEEEEEE
Q 045299 562 -TEPQPGLLRVVI 573 (574)
Q Consensus 562 -~E~n~G~L~V~L 573 (574)
.+-+.|+.+|.|
T Consensus 769 ~~~GG~Gat~V~l 781 (782)
T PRK00409 769 PNEGGFGVTIVEL 781 (782)
T ss_pred cccCCCeEEEEEE
Confidence 234689998876
No 8
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=97.53 E-value=0.00021 Score=83.13 Aligned_cols=71 Identities=27% Similarity=0.305 Sum_probs=56.9
Q ss_pred ceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCC--cc-----
Q 045299 489 DRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGL--DY----- 561 (574)
Q Consensus 489 ~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~--~f----- 561 (574)
...|||||++++||+..|+.+|..+. ..| ...|+||+|+|. ..|+.+|..||. ++.+ .|
T Consensus 693 ~~~ldl~G~~~~eA~~~l~~~ld~a~----~~g-~~~v~IIHGkGt--------G~Lr~~v~~~L~-~~~~V~~f~~a~~ 758 (771)
T TIGR01069 693 SLTLDLRGQRSEEALDRLEKFLNDAL----LAG-YEVVLIIHGKGS--------GKLRKGVQELLK-NHPKVKSFRDAPP 758 (771)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHH----HCC-CCEEEEEcCCCh--------hHHHHHHHHHhc-CCcceeeecccCc
Confidence 56899999999999999999998853 234 478999999983 479999999999 6643 23
Q ss_pred ccCCCcEEEEEE
Q 045299 562 TEPQPGLLRVVI 573 (574)
Q Consensus 562 ~E~n~G~L~V~L 573 (574)
.+-+.|+.+|.|
T Consensus 759 ~~GG~G~t~V~l 770 (771)
T TIGR01069 759 NDGGSGVTIVYL 770 (771)
T ss_pred ccCCceEEEEEE
Confidence 244688888876
No 9
>PF07145 PAM2: Ataxin-2 C-terminal region; InterPro: IPR009818 This entry represents a conserved region approximately 250 residues long located towards the C terminus of eukaryotic ataxin-2. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].; PDB: 3NTW_B 1JH4_B 3KTR_B 3KUJ_B 3KUT_D 3KUS_D 1JGN_B 2RQG_A 2RQH_A.
Probab=97.46 E-value=5.2e-05 Score=48.30 Aligned_cols=16 Identities=69% Similarity=1.005 Sum_probs=12.4
Q ss_pred cccccCCCcccccccc
Q 045299 20 KATALNPNAAEFVPFS 35 (574)
Q Consensus 20 ~~t~lnpnaaefvp~~ 35 (574)
+.+.|||||.||||++
T Consensus 2 ~~s~LNp~A~eFvP~~ 17 (18)
T PF07145_consen 2 KSSKLNPNAPEFVPSS 17 (18)
T ss_dssp -SSSSSTTSSSS-TTT
T ss_pred cccccCCCCccccCCC
Confidence 3568999999999986
No 10
>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=96.00 E-value=0.012 Score=44.34 Aligned_cols=36 Identities=31% Similarity=0.458 Sum_probs=33.2
Q ss_pred hhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHHHh
Q 045299 223 VEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLTQ 258 (574)
Q Consensus 223 lefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L~~ 258 (574)
|+.|.+.||.++.+.|..++.+|++++++||++|-+
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 788999999999999999999999999999999954
No 11
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=94.32 E-value=0.065 Score=40.35 Aligned_cols=35 Identities=29% Similarity=0.365 Sum_probs=33.6
Q ss_pred hhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHHH
Q 045299 223 VEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLT 257 (574)
Q Consensus 223 lefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L~ 257 (574)
++.|...||.++.+.|..++.+++++++.||++|-
T Consensus 6 v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 6 LHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 88999999999999999999999999999999994
No 12
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=90.71 E-value=0.42 Score=36.43 Aligned_cols=37 Identities=22% Similarity=0.316 Sum_probs=35.3
Q ss_pred CCchhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHH
Q 045299 220 MNPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEML 256 (574)
Q Consensus 220 ~dplefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L 256 (574)
++|+|.|+.-||.-....|..+...+++|+-.+||.+
T Consensus 2 r~pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 2 RSPIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CCHHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHHh
Confidence 5799999999999999999999999999999999976
No 13
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=89.59 E-value=0.69 Score=54.49 Aligned_cols=71 Identities=27% Similarity=0.325 Sum_probs=53.8
Q ss_pred ceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCC----Cccc--
Q 045299 489 DRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEG----LDYT-- 562 (574)
Q Consensus 489 ~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g----~~f~-- 562 (574)
...+||+|..+.+|+..|+..+..+-- .| -.+++||.|.| . .+|+..|.+||+ ++. +++-
T Consensus 676 ~~~ldLrg~r~e~a~~~l~k~i~eail----~~-~~~v~iihgkG------t--G~lre~v~~~Lk-~~~~v~~~~~~~~ 741 (753)
T COG1193 676 SNRLDLRGERSEEALDELDKSIDEAIL----EG-YEKVSIIHGKG------T--GKLREGVQEYLK-KHKKVKSFRDAPP 741 (753)
T ss_pred cccccccccccHHHHHHHHhhhHHHHH----cC-CcceeEEeeee------c--hHHHHHHHHHHH-hCCCccCcCCCCc
Confidence 379999999999999999999988531 22 36899999985 3 799999999999 553 2332
Q ss_pred -cCCCcEEEEEE
Q 045299 563 -EPQPGLLRVVI 573 (574)
Q Consensus 563 -E~n~G~L~V~L 573 (574)
+-..|+-+|.|
T Consensus 742 ~~GG~G~tiv~l 753 (753)
T COG1193 742 NEGGSGVTIVEL 753 (753)
T ss_pred CCCCCCeeEEeC
Confidence 33466666654
No 14
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=71.91 E-value=15 Score=36.50 Aligned_cols=89 Identities=20% Similarity=0.242 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcccCCCCCCceeeecCCCCHHHHHHH
Q 045299 426 RLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRNPVELQGNGRGQDRMIDLHGLHVSEAIHV 505 (574)
Q Consensus 426 ~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAAeaIf~~RN~~~~qG~g~~~~~~IDLHGLhV~EAv~i 505 (574)
....+.+.+..++|..||...-..+..+-. ......+.|+..||.. +
T Consensus 170 ~~~~~~~~~~~~~~~~gd~~~l~~~~~~~~--------~~p~~~~~ll~~RN~~-------------------------~ 216 (259)
T PF01963_consen 170 EDGEKMLEQLIEAWKNGDLDALMELMKEDE--------SFPELYEVLLDERNRR-------------------------W 216 (259)
T ss_pred ccchHHHHHHHHHHHccCHHHHHHHHHhcc--------cCHHHHHHHHHHHhHH-------------------------H
Confidence 444677889999999999643332211100 4455567788888843 2
Q ss_pred HHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCcccc
Q 045299 506 LKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYTE 563 (574)
Q Consensus 506 Lk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~E 563 (574)
++.....+. ..+.+.|++|.||-..-+ -|.+.|+ +.||.++.
T Consensus 217 ~~~i~~~l~-------~~~~~fvvVGa~HL~G~~--------gvl~lLr-~~Gy~V~~ 258 (259)
T PF01963_consen 217 AEKIEELLK-------EGGTVFVVVGAGHLPGED--------GVLDLLR-KKGYTVEP 258 (259)
T ss_pred HHHHHHHHh-------cCCCEEEEEcchhccchh--------hHHHHHH-hCCceeec
Confidence 222222221 124789999999886544 2667898 99998853
No 15
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=70.27 E-value=1.8 Score=47.75 Aligned_cols=136 Identities=16% Similarity=0.074 Sum_probs=108.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcccCCCCCCce
Q 045299 411 ANMYSELREEARDHARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRNPVELQGNGRGQDR 490 (574)
Q Consensus 411 ~~~Y~e~R~eA~~~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAAeaIf~~RN~~~~qG~g~~~~~ 490 (574)
..+|...+.+......++...+...+-|+..+....+..++.+.+.....++....++....|...+... ...
T Consensus 240 ~~~~~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~s~~-------~~~ 312 (448)
T KOG2401|consen 240 LEELQKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNKESIK-------SER 312 (448)
T ss_pred hhhcchhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhhhhhh-------hhH
Confidence 5677778888888888888999999999998989999999999999999999988888888776555443 578
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCcc
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDY 561 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f 561 (574)
.+|+|++.+..|...+...+...-.. ....+.++.+.++|...++ +++++++..++. .+.+..
T Consensus 313 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~v--~~~~~a~~~~~~-~~~~~r 375 (448)
T KOG2401|consen 313 EIDNQRLYKKAAEQKAQPEIEDAINL-----QASELKPKVSLAVKGSYAV--AKLKPATQWKLD-NEEIER 375 (448)
T ss_pred HhhhhhHHHHHHHhhhhhhhhhhhhh-----hhhhhchhhhhcccccchh--hhcchHHHHHHh-hhhhhc
Confidence 89999988888887777666542111 1245778889999999888 999999999998 776664
No 16
>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=67.83 E-value=8.8 Score=27.96 Aligned_cols=32 Identities=25% Similarity=0.342 Sum_probs=27.3
Q ss_pred hhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHH
Q 045299 223 VEFLASQFPGFAAESLAEVYFANGCDLNLTIEML 256 (574)
Q Consensus 223 lefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L 256 (574)
|.-|+.. ||+.+....|+..++.+++.+|+.|
T Consensus 6 v~~L~~m--Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 6 VQQLMEM--GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHH--TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 5556666 9999999999999999999999986
No 17
>PLN03218 maturation of RBCL 1; Provisional
Probab=63.79 E-value=13 Score=45.66 Aligned_cols=81 Identities=31% Similarity=0.251 Sum_probs=58.1
Q ss_pred CceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCC-cceEE---------EEEcCCCCCCCCCCCCCcHHHHHHHHHhcC
Q 045299 488 QDRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQ-RLQVY---------ICVGTGHHTRGSRTPVRLPIAVQRYLLEEE 557 (574)
Q Consensus 488 ~~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~-~~~L~---------IITG~G~HS~gG~~~arLkpAV~~~L~~e~ 557 (574)
..+.||+|.|.|.-|.-.|-.-|+.++..- ..|. -..+. |-||+|.|+..-- .++..+|...|+ +.
T Consensus 920 ~~~~~d~~~~~~~aa~~~l~~wl~~~~~~~-~~g~~lp~~~~~~~~~~~~~~~~~g~~~~~~~--~~~~~~~~~~l~-~l 995 (1060)
T PLN03218 920 SPIVIDAEELPVFAAEVYLLTILKGLKHRL-AAGAKLPNVTILLPTEKKEIYTPKGEKTINLA--GRVGQAVAALLR-RL 995 (1060)
T ss_pred CceEEEcccCcchhHHHHHHHHHHHHHHHH-hccCcCCcceeeeccccceeeccCCchhHHHH--HHHHHHHHHHHH-Hh
Confidence 479999999999999999998888886532 2332 22333 4566666654433 578899999999 99
Q ss_pred CCcccc-CCCcEEEEE
Q 045299 558 GLDYTE-PQPGLLRVV 572 (574)
Q Consensus 558 g~~f~E-~n~G~L~V~ 572 (574)
+++|.+ +..|.|+++
T Consensus 996 ~~~~~~~~~~g~~~~~ 1011 (1060)
T PLN03218 996 GLPYQGSESHGKLRIN 1011 (1060)
T ss_pred CCCCCCCCCCCeEEec
Confidence 999964 234888764
No 18
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=61.43 E-value=7.1 Score=36.25 Aligned_cols=37 Identities=27% Similarity=0.310 Sum_probs=34.2
Q ss_pred CCCchhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHHH
Q 045299 219 EMNPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLT 257 (574)
Q Consensus 219 ~~dplefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L~ 257 (574)
+.| |++++.++ |+|.+....|+-.|++||-.+|-.|.
T Consensus 77 ~ed-I~lv~~q~-gvs~~~A~~AL~~~~gDl~~AI~~L~ 113 (115)
T PRK06369 77 EED-IELVAEQT-GVSEEEARKALEEANGDLAEAILKLS 113 (115)
T ss_pred HHH-HHHHHHHH-CcCHHHHHHHHHHcCCcHHHHHHHHh
Confidence 556 99999999 89999999999999999999998885
No 19
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=59.68 E-value=9 Score=35.67 Aligned_cols=37 Identities=24% Similarity=0.253 Sum_probs=34.0
Q ss_pred CCCchhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHHH
Q 045299 219 EMNPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLT 257 (574)
Q Consensus 219 ~~dplefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L~ 257 (574)
+.| +++|++++ |+|.+...+|+.+|++||-.+|-.|.
T Consensus 79 ~eD-I~lV~eq~-gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 79 EDD-IELVMKQC-NVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred HHH-HHHHHHHh-CcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 456 99999999 89999999999999999999998874
No 20
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=59.07 E-value=36 Score=27.20 Aligned_cols=65 Identities=22% Similarity=0.330 Sum_probs=45.5
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc--cCCCcE
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT--EPQPGL 568 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~--E~n~G~ 568 (574)
.||+-|+.=.+-+-.+++.|..+. .| ..+.|++.. +--..-|.+|+. +.|+.+. +...|.
T Consensus 1 ~lD~rg~~CP~Pl~~~~~~l~~l~-----~g--~~l~v~~d~----------~~~~~~i~~~~~-~~g~~~~~~~~~~~~ 62 (69)
T cd00291 1 TLDLRGLPCPLPVLKTKKALEKLK-----SG--EVLEVLLDD----------PGAVEDIPAWAK-ETGHEVLEVEEEGGV 62 (69)
T ss_pred CccccCCcCCHHHHHHHHHHhcCC-----CC--CEEEEEecC----------CcHHHHHHHHHH-HcCCEEEEEEEeCCE
Confidence 489999999988888888887642 23 457777653 222456889999 9999984 334566
Q ss_pred EEEEE
Q 045299 569 LRVVI 573 (574)
Q Consensus 569 L~V~L 573 (574)
+.+.|
T Consensus 63 ~~i~i 67 (69)
T cd00291 63 YRILI 67 (69)
T ss_pred EEEEE
Confidence 66654
No 21
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=59.04 E-value=14 Score=26.49 Aligned_cols=25 Identities=24% Similarity=0.321 Sum_probs=23.7
Q ss_pred CCcHHHHHHHHHHcCCCHHHHHHHH
Q 045299 232 GFAAESLAEVYFANGCDLNLTIEML 256 (574)
Q Consensus 232 g~s~esl~s~Y~aNg~sl~aTI~~L 256 (574)
||+.+.+..+++.++.|++.+++.|
T Consensus 12 Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 12 GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 8999999999999999999999887
No 22
>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=58.62 E-value=15 Score=26.50 Aligned_cols=26 Identities=23% Similarity=0.353 Sum_probs=24.4
Q ss_pred CCcHHHHHHHHHHcCCCHHHHHHHHH
Q 045299 232 GFAAESLAEVYFANGCDLNLTIEMLT 257 (574)
Q Consensus 232 g~s~esl~s~Y~aNg~sl~aTI~~L~ 257 (574)
||+.+.+..+++.+++|++.+++.|.
T Consensus 12 Gf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 12 GFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 89999999999999999999999884
No 23
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=55.58 E-value=39 Score=27.78 Aligned_cols=65 Identities=25% Similarity=0.329 Sum_probs=47.9
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc--cCCCcE
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT--EPQPGL 568 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~--E~n~G~ 568 (574)
.||+.|+.=..-+-.+++.|..+. .| ..|.|++.- +--..-|.+|+. +.|+.+. +...|.
T Consensus 1 ~lD~rG~~CP~Pvl~~kkal~~l~-----~G--~~l~V~~d~----------~~a~~di~~~~~-~~G~~~~~~~~~~~~ 62 (69)
T cd03420 1 EVDACGLQCPGPILKLKKEIDKLQ-----DG--EQLEVKASD----------PGFARDAQAWCK-STGNTLISLETEKGK 62 (69)
T ss_pred CcccCCCcCCHHHHHHHHHHHcCC-----CC--CEEEEEECC----------ccHHHHHHHHHH-HcCCEEEEEEecCCE
Confidence 489999998888888898887752 23 467777753 223456899999 9999984 335788
Q ss_pred EEEEE
Q 045299 569 LRVVI 573 (574)
Q Consensus 569 L~V~L 573 (574)
+.+.|
T Consensus 63 ~~~~I 67 (69)
T cd03420 63 VKAVI 67 (69)
T ss_pred EEEEE
Confidence 88875
No 24
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=53.69 E-value=61 Score=26.88 Aligned_cols=39 Identities=21% Similarity=0.185 Sum_probs=29.0
Q ss_pred HHHHHHHHH-HHHHHHHhcCHHHHHHHHHHHHHHHHHHHH
Q 045299 425 ARLRNAYFE-QARQAYLIGNKALAKELSVKGQLHNMQMKA 463 (574)
Q Consensus 425 a~~Rne~f~-kAaqAyrrGdka~Ak~LSekGr~~~~qmke 463 (574)
...|.+-|. .|.+|-+.||.+.|+.|-..++.+....+.
T Consensus 4 L~~R~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 4 LQQRQEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 344544454 477899999999999999888888665554
No 25
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=53.01 E-value=25 Score=28.50 Aligned_cols=65 Identities=25% Similarity=0.344 Sum_probs=47.0
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc--cCCCcE
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT--EPQPGL 568 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~--E~n~G~ 568 (574)
+||+-|+.=..-+-.+++.|..+. .| ..|.|++-- +--..-|.+|+. +.|+.+. +...|.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~-----~G--~~l~v~~d~----------~~~~~di~~~~~-~~g~~~~~~~~~~~~ 63 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP-----PG--EVLEVLVDD----------PAAVEDIPRWCE-ENGYEVVEVEEEGGE 63 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG-----TT---EEEEEESS----------TTHHHHHHHHHH-HHTEEEEEEEESSSS
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC-----CC--CEEEEEECC----------ccHHHHHHHHHH-HCCCEEEEEEEeCCE
Confidence 689999999999989998887752 33 467777754 333567999999 9999863 236787
Q ss_pred EEEEE
Q 045299 569 LRVVI 573 (574)
Q Consensus 569 L~V~L 573 (574)
+.+.|
T Consensus 64 ~~i~I 68 (70)
T PF01206_consen 64 YRILI 68 (70)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 77765
No 26
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=51.18 E-value=18 Score=31.28 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHH
Q 045299 433 EQARQAYLIGNKALAKELSVKGQLHNM 459 (574)
Q Consensus 433 ~kAaqAyrrGdka~Ak~LSekGr~~~~ 459 (574)
.|+..+|++||.+.|.+.|+++|.+..
T Consensus 42 ~kv~~~~~~Gd~~~A~~aS~~Ak~~~~ 68 (82)
T PF04505_consen 42 SKVRSRYAAGDYEGARRASRKAKKWSI 68 (82)
T ss_pred hhhHHHHHCCCHHHHHHHHHHhHHHHH
Confidence 588999999999999999999998864
No 27
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=49.09 E-value=1.2e+02 Score=26.56 Aligned_cols=44 Identities=16% Similarity=0.117 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 045299 424 HARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGK 467 (574)
Q Consensus 424 ~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~k 467 (574)
.+..-.+.+.+|..+|..|+...|..|..+++.+.+.++..-..
T Consensus 41 el~~A~~~L~~A~~a~~~~~y~~A~~~A~~A~~~A~~A~~~a~~ 84 (103)
T PF14346_consen 41 ELKEAREKLQRAKAALDDGDYERARRLAEQAQADAELAEAKAEA 84 (103)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455577889999999999999999999999886665554433
No 28
>PF10862 FcoT: FcoT-like thioesterase domain; InterPro: IPR022598 Proteins in this family have a HotDog fold. This family was formerly known as DUF2662. The structure of Rv0098 from M. tuberculosis [] suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups []. The maximal Kcat was observed for palmitoyl-CoA, although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.; PDB: 2PFC_A 3B18_A.
Probab=48.43 E-value=2.6 Score=40.94 Aligned_cols=19 Identities=32% Similarity=0.691 Sum_probs=15.5
Q ss_pred HHHHHhhCCCCCCCCcccc
Q 045299 81 HQYWRHQLPDDITPDFKVL 99 (574)
Q Consensus 81 ~~~w~~qlpddi~pdf~~~ 99 (574)
-+||++||||=+|-+|+.-
T Consensus 86 ddf~~rQLsdilI~~~~S~ 104 (157)
T PF10862_consen 86 DDFWERQLSDILITSFKSR 104 (157)
T ss_dssp HHHHHCHHHHEEEEEE-EE
T ss_pred HHHHHhhcCceeEeechhh
Confidence 3799999999999997653
No 29
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=43.70 E-value=42 Score=31.35 Aligned_cols=37 Identities=14% Similarity=0.173 Sum_probs=27.7
Q ss_pred ceEEEEEcCCCCCCC-CCCCCC----cHHHHHHHHHhcCCCcccc
Q 045299 524 LQVYICVGTGHHTRG-SRTPVR----LPIAVQRYLLEEEGLDYTE 563 (574)
Q Consensus 524 ~~L~IITG~G~HS~g-G~~~ar----LkpAV~~~L~~e~g~~f~E 563 (574)
..+.|+|||..+... +. ++ .-+.+.+||. +++++|.+
T Consensus 41 ~~IiiaTGR~~~~~~~n~--~~i~~~~~~~t~~wL~-k~~ipYd~ 82 (126)
T TIGR01689 41 FEIVISSSRNMRTYEGNV--GKINIHTLPIIILWLN-QHNVPYDE 82 (126)
T ss_pred CEEEEECCCCchhhhccc--cccchhhHHHHHHHHH-HcCCCCce
Confidence 469999999988643 22 33 3458899999 99999964
No 30
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=42.93 E-value=23 Score=33.27 Aligned_cols=37 Identities=27% Similarity=0.324 Sum_probs=34.2
Q ss_pred CCCchhhhhhcCCCCcHHHHHHHHHHcCCCHHHHHHHHH
Q 045299 219 EMNPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLT 257 (574)
Q Consensus 219 ~~dplefl~s~fpg~s~esl~s~Y~aNg~sl~aTI~~L~ 257 (574)
+.| ++++..++ |.|.+....|+.++|+||..+|--|+
T Consensus 85 eeD-IkLV~eQa-~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 85 EED-IKLVMEQA-GVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred HHH-HHHHHHHh-CCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 456 99999999 89999999999999999999998885
No 31
>PF03357 Snf7: Snf7; InterPro: IPR005024 This is a family of eukaryotic proteins which are variously described as either hypothetical protein, developmental protein or related to yeast SNF7. The family contains human CHMP1. CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), is encoded by an alternative open reading frame in the PRSM1 gene [] and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localisation signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. Human CHMP1 is strongly implicated in multivesicular body formation. A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. Immunocytochemistry and biochemical fractionation localise CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, over expression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae (Baker's yeast) further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homologue of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes []. ; GO: 0015031 protein transport; PDB: 2V6X_B 2W2U_D 2GD5_D 3FRT_B 3FRV_A 4ABM_D 3EAB_H 3HTU_D.
Probab=41.04 E-value=1.7e+02 Score=27.23 Aligned_cols=57 Identities=16% Similarity=0.122 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045299 413 MYSELREEARDHARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQ 469 (574)
Q Consensus 413 ~Y~e~R~eA~~~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAA 469 (574)
.-..+...+..+-..-.++..+|..+.+.|++..|+.|..+-+.+.++.........
T Consensus 9 ~~~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~~~ 65 (171)
T PF03357_consen 9 TIRRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQLS 65 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566677777788888999999999999999999999888877776666555433
No 32
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=39.25 E-value=84 Score=25.78 Aligned_cols=64 Identities=16% Similarity=0.289 Sum_probs=45.5
Q ss_pred eecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc--cCCCcEE
Q 045299 492 IDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT--EPQPGLL 569 (574)
Q Consensus 492 IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~--E~n~G~L 569 (574)
||+-|+.=..=+-.+++.|..+. .| ..|.|++.- +--..-|.+|++ +.|+.+. +..+|.+
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~-----~G--~~l~V~~dd----------~~s~~di~~~~~-~~g~~~~~~~~~~~~~ 63 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK-----PG--DTLLVLATD----------PSTTRDIPKFCT-FLGHELLAQETEDEPY 63 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC-----CC--CEEEEEeCC----------CchHHHHHHHHH-HcCCEEEEEEEcCCEE
Confidence 78888888888888888887652 23 356776653 223446889999 9999985 3357888
Q ss_pred EEEE
Q 045299 570 RVVI 573 (574)
Q Consensus 570 ~V~L 573 (574)
.+.|
T Consensus 64 ~~~I 67 (69)
T cd03423 64 RYLI 67 (69)
T ss_pred EEEE
Confidence 7765
No 33
>PF13763 DUF4167: Domain of unknown function (DUF4167)
Probab=37.38 E-value=1.3e+02 Score=26.51 Aligned_cols=38 Identities=24% Similarity=0.248 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 045299 430 AYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGK 467 (574)
Q Consensus 430 e~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~k 467 (574)
+|.+.|++|-..||+-+|..|.+-|..|...+.++...
T Consensus 41 KY~~LArDA~ssGDrV~aEny~QHAeHY~Ril~~~~~~ 78 (80)
T PF13763_consen 41 KYNQLARDAQSSGDRVLAENYLQHAEHYFRILAAAQAQ 78 (80)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56677888999999999999999999998877766543
No 34
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=36.66 E-value=1.3e+02 Score=25.76 Aligned_cols=68 Identities=15% Similarity=0.222 Sum_probs=49.8
Q ss_pred CceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc--cCC
Q 045299 488 QDRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT--EPQ 565 (574)
Q Consensus 488 ~~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~--E~n 565 (574)
.+.+||+-|+.=..=+-.+++.|..+. .| ..|.|++.- +--+.-|..|++ +.|+++. +..
T Consensus 8 ~~~~lD~~Gl~CP~Pll~~kk~l~~l~-----~G--~~l~V~~dd----------~~~~~di~~~~~-~~G~~~~~~~~~ 69 (81)
T PRK00299 8 PDHTLDALGLRCPEPVMMVRKTVRNMQ-----PG--ETLLIIADD----------PATTRDIPSFCR-FMDHELLAQETE 69 (81)
T ss_pred cCeEEecCCCCCCHHHHHHHHHHHcCC-----CC--CEEEEEeCC----------ccHHHHHHHHHH-HcCCEEEEEEec
Confidence 467899999999988888998887752 33 356676642 233556889998 9999984 445
Q ss_pred CcEEEEEE
Q 045299 566 PGLLRVVI 573 (574)
Q Consensus 566 ~G~L~V~L 573 (574)
.|.+.+.|
T Consensus 70 ~g~~~~~I 77 (81)
T PRK00299 70 QLPYRYLI 77 (81)
T ss_pred CCEEEEEE
Confidence 78887765
No 35
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=35.78 E-value=1.5e+02 Score=23.94 Aligned_cols=64 Identities=25% Similarity=0.353 Sum_probs=43.5
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc-cCCCcEE
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT-EPQPGLL 569 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~-E~n~G~L 569 (574)
.||+-|+.=.+-+-.+++.| .+. .| ..|.|++-- +--..-|.+|+. +.|+.+. +...|.+
T Consensus 1 ~lD~rG~~CP~P~l~~k~al-~~~-----~g--~~l~v~~d~----------~~s~~~i~~~~~-~~G~~~~~~~~~~~~ 61 (67)
T cd03421 1 TIDARGLACPQPVIKTKKAL-ELE-----AG--GEIEVLVDN----------EVAKENVSRFAE-SRGYEVSVEEKGGEF 61 (67)
T ss_pred CcccCCCCCCHHHHHHHHHH-hcC-----CC--CEEEEEEcC----------hhHHHHHHHHHH-HcCCEEEEEecCCEE
Confidence 48999999999998999888 542 23 356666432 112336889999 9999984 2344566
Q ss_pred EEEE
Q 045299 570 RVVI 573 (574)
Q Consensus 570 ~V~L 573 (574)
.|.|
T Consensus 62 ~i~I 65 (67)
T cd03421 62 EITI 65 (67)
T ss_pred EEEE
Confidence 6654
No 36
>PRK11018 hypothetical protein; Provisional
Probab=30.64 E-value=1.9e+02 Score=24.49 Aligned_cols=68 Identities=13% Similarity=0.091 Sum_probs=47.8
Q ss_pred CceeeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCccc--cCC
Q 045299 488 QDRMIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYT--EPQ 565 (574)
Q Consensus 488 ~~~~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~--E~n 565 (574)
.+.+||+-|+.=..=+-.+++.|..+. .| ..|.|++-- +--..-|..|++ +.|+++. +..
T Consensus 7 ~~~~lD~rG~~CP~Pvl~~kk~l~~l~-----~G--~~L~V~~d~----------~~a~~di~~~~~-~~G~~v~~~~~~ 68 (78)
T PRK11018 7 PDYRLDMVGEPCPYPAVATLEALPQLK-----KG--EILEVVSDC----------PQSINNIPLDAR-NHGYTVLDIQQD 68 (78)
T ss_pred CCeeEECCCCcCCHHHHHHHHHHHhCC-----CC--CEEEEEeCC----------ccHHHHHHHHHH-HcCCEEEEEEec
Confidence 467899999998888888888887652 34 346665432 122346889999 9999984 445
Q ss_pred CcEEEEEE
Q 045299 566 PGLLRVVI 573 (574)
Q Consensus 566 ~G~L~V~L 573 (574)
.|.+.+.|
T Consensus 69 ~g~~~~~I 76 (78)
T PRK11018 69 GPTIRYLI 76 (78)
T ss_pred CCeEEEEE
Confidence 68887765
No 37
>PF10006 DUF2249: Uncharacterized conserved protein (DUF2249); InterPro: IPR018720 This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see IPR001455 from INTERPRO).
Probab=29.63 E-value=1.5e+02 Score=24.20 Aligned_cols=63 Identities=27% Similarity=0.375 Sum_probs=41.8
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcC-CC-cc--ccCCC
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEE-GL-DY--TEPQP 566 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~-g~-~f--~E~n~ 566 (574)
+||+.||...+....+-+.+..|. .| ..|.||.=. -+.-+-..|. .. |+ .| .+..+
T Consensus 1 ~LDvR~l~~~~p~~~il~~~~~L~-----~G--e~l~lv~d~------------~P~pL~~~l~-~~~g~~~~~~~~~~~ 60 (69)
T PF10006_consen 1 VLDVRGLPPPEPHERILEALDELP-----PG--ETLELVNDH------------DPRPLYPQLE-ERRGFFSWEYEEQGP 60 (69)
T ss_pred CEECCCCCCcChHHHHHHHHHcCC-----CC--CEEEEEeCC------------CCHHHHHHHH-HhCCCceEEEEEcCC
Confidence 589999999999988888887763 34 346666322 1222444455 45 65 55 56778
Q ss_pred cEEEEEE
Q 045299 567 GLLRVVI 573 (574)
Q Consensus 567 G~L~V~L 573 (574)
|...|.|
T Consensus 61 ~~w~v~i 67 (69)
T PF10006_consen 61 GEWRVRI 67 (69)
T ss_pred CEEEEEE
Confidence 8888876
No 38
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=27.92 E-value=3.1e+02 Score=24.15 Aligned_cols=59 Identities=17% Similarity=0.148 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045299 409 AVANMYSELREEARDHARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQ 469 (574)
Q Consensus 409 a~~~~Y~e~R~eA~~~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAA 469 (574)
.....+.++..+.......||.+-.+-.++...| ..+..+..+++....++++...+..
T Consensus 33 ~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~~ 91 (108)
T PF02403_consen 33 ELDQERRELQQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQLK 91 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4467777888888999999999998888888887 4556666777777776666655443
No 39
>PRK06851 hypothetical protein; Provisional
Probab=27.56 E-value=5.2e+02 Score=28.48 Aligned_cols=128 Identities=10% Similarity=0.104 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcccCCCCCCce
Q 045299 413 MYSELREEARDHARLRNAYFEQARQAYLIGNK--ALAKELSVKGQLHNMQMKAAHGKAQESIYRQRNPVELQGNGRGQDR 490 (574)
Q Consensus 413 ~Y~e~R~eA~~~a~~Rne~f~kAaqAyrrGdk--a~Ak~LSekGr~~~~qmkean~kAAeaIf~~RN~~~~qG~g~~~~~ 490 (574)
.-.++|++..+......+||++|.+.+..... ..-..+-... .-.+++.+.-++=...||....... ..+...
T Consensus 116 ~l~~~k~eI~~~~~~~~~~~~~Ay~~l~~A~~ihdd~e~~y~~~-md~~k~~~~~~~l~~~l~~~~~~~~----~~g~~r 190 (367)
T PRK06851 116 KLRKHKEEILKINEEISRCFQRAYEYLNEALAIHDEWEKIYIEN-MDFAKANELTDELIQELFKGAPGKI----SKGKVR 190 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHhccCcccc----cCCcee
Confidence 34567888888888888999998888766531 0001111110 1134444445555556676543210 013467
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCcc
Q 045299 491 MIDLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDY 561 (574)
Q Consensus 491 ~IDLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f 561 (574)
.+=+.|.+..-.+..++..+..+ ..+++|||. ..-|+ .-|-..|.+.+. +.|+.+
T Consensus 191 h~F~ga~Tp~G~~s~~~~l~~~~----------~~~~~i~G~---pG~GK--stl~~~i~~~a~-~~G~~v 245 (367)
T PRK06851 191 HLFLGAITPKGAVDFVPSLTEGV----------KNRYFLKGR---PGTGK--STMLKKIAKAAE-ERGFDV 245 (367)
T ss_pred eeeccccCCCcHHhhHHhHhccc----------ceEEEEeCC---CCCcH--HHHHHHHHHHHH-hCCCeE
Confidence 77789999999998888766332 467889885 11222 445556666676 788875
No 40
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=24.68 E-value=2.6e+02 Score=26.17 Aligned_cols=39 Identities=23% Similarity=0.238 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Q 045299 417 LREEARDHARLRNAYFEQARQAYLIGNKALAKELSVKGQ 455 (574)
Q Consensus 417 ~R~eA~~~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr 455 (574)
.|.++..+.+.....+..|...+..|+...|-++++|+=
T Consensus 2 ~~~~~~~~~~rA~~~l~~A~~~le~G~y~~a~f~aqQAv 40 (132)
T COG2250 2 MREEAEKWLRRAERDLKLAKRDLELGDYDLACFHAQQAV 40 (132)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence 367788888888899999999999999999999987754
No 41
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.83 E-value=5.3e+02 Score=30.22 Aligned_cols=55 Identities=16% Similarity=0.166 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCC
Q 045299 499 VSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGL 559 (574)
Q Consensus 499 V~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~ 559 (574)
..+|....+.++..-+. ..+.....++.-+.----.|++ -.|+|.+-.-|. ..++
T Consensus 55 ~~~~~~~~~~~~~~~~~---~~~g~~~~~~~~~~~~~~~GdK--I~LPpSaL~~L~-~~~~ 109 (567)
T PLN03086 55 AIEAQIKADQQMQESLQ---AGRGIVFSRIFEAVSFQGNGDK--IKLPPSCFTELS-DQGA 109 (567)
T ss_pred HHHHHHHHHHHHHHHHH---cCCCeEEEEEeeccccCCCCCe--EEcCHHHHHHHH-hcCC
Confidence 34444445555544322 1222233334433322224555 788999988888 6665
No 42
>PF09507 CDC27: DNA polymerase subunit Cdc27; InterPro: IPR019038 This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. ; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 1U76_B 3E0J_B.
Probab=22.77 E-value=1.1e+02 Score=32.87 Aligned_cols=40 Identities=20% Similarity=0.257 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCC
Q 045299 496 GLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTR 537 (574)
Q Consensus 496 GLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~ 537 (574)
++||..|-+||.+|+...+.. ..+.....|||||+-.+..
T Consensus 13 ~ihvn~AK~~L~ef~~~~~~k--~~~~l~atYlvsG~~k~~~ 52 (430)
T PF09507_consen 13 GIHVNQAKQMLYEFHEKQNAK--KPGSLHATYLVSGWLKDNG 52 (430)
T ss_dssp T--HHHHHHHHHHHHHHHHHH--HS-S-EEEEEEEEEEESSS
T ss_pred CCCHHHHHHHHHHHHHhcccc--CCCceEEEEEEEEEeCCCC
Confidence 579999999999999886422 1244567899999977654
No 43
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=22.06 E-value=78 Score=29.16 Aligned_cols=50 Identities=24% Similarity=0.421 Sum_probs=35.8
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHHHHHhCCcceEEEEEcCCCCCCCCCCCCCcHHHHHHHHHhcCCCcccc
Q 045299 493 DLHGLHVSEAIHVLKHELSVLRSTARAAGQRLQVYICVGTGHHTRGSRTPVRLPIAVQRYLLEEEGLDYTE 563 (574)
Q Consensus 493 DLHGLhV~EAv~iLk~~L~~Lr~~ar~~g~~~~L~IITG~G~HS~gG~~~arLkpAV~~~L~~e~g~~f~E 563 (574)
+.|.|..++...+|+.. .. .||.|+|.+-. -.+.|++.++|. +.|+.+..
T Consensus 42 ~~~~l~~~~l~~ll~~~--------------pe-ivliGTG~~~~-----~~~~~~~~~~l~-~~Gi~ve~ 91 (117)
T cd05126 42 TSHGLQPEELEELLEEG--------------VE-VIVIGTGQSGA-----LKVPPETVEKLE-KRGVEVLV 91 (117)
T ss_pred CcccCCHHHHHHHHhcC--------------CC-EEEEcCCCCcc-----ccCCHHHHHHHH-hcCCEEEE
Confidence 88899988866555411 12 57789987644 256889999999 99998743
No 44
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.57 E-value=2.8e+02 Score=25.69 Aligned_cols=40 Identities=15% Similarity=0.207 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Q 045299 422 RDHARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMK 462 (574)
Q Consensus 422 ~~~a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmk 462 (574)
..+...-+.+|+.|..+++.| ..+|..|-+.++...++++
T Consensus 8 kia~eRi~~L~~lA~~~~~~~-~~laRrYv~la~~Is~K~r 47 (105)
T COG2023 8 KIAAERIDYLYSLAEETFRTG-PDLARRYVKLARRISMKYR 47 (105)
T ss_pred HHHHHHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHHhhc
Confidence 344445568899999999999 7788777777666555443
No 45
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=20.89 E-value=3.1e+02 Score=24.74 Aligned_cols=67 Identities=16% Similarity=0.156 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcccCCCCCCceeeecCCCCHHHHHH
Q 045299 425 ARLRNAYFEQARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRNPVELQGNGRGQDRMIDLHGLHVSEAIH 504 (574)
Q Consensus 425 a~~Rne~f~kAaqAyrrGdka~Ak~LSekGr~~~~qmkean~kAAeaIf~~RN~~~~qG~g~~~~~~IDLHGLhV~EAv~ 504 (574)
+..| .++-+|-++.+.||...|.++-.+|++....+-+.| .+-|-.+-+ +....++|==.|.++-+.
T Consensus 15 G~Ar-s~~~eAl~~a~~gdfe~A~~~l~eA~~~l~~AH~~q---t~liq~ea~---------g~~~~~slLlvHAQDhLM 81 (99)
T TIGR00823 15 GDAR-SKALEALKAAKAGDFAKARALVEQAGMCLNEAHLAQ---TSLLAQEAG---------GGKMEVSLTMVHAQDHLM 81 (99)
T ss_pred HHHH-HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhc---------CCCCccceeehhHHHHHH
Confidence 3444 556689999999999999999999887655544444 444433322 134445555556555444
Done!