Query 018937
Match_columns 348
No_of_seqs 263 out of 650
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:18:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018937hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0010 Ubiquitin-like protein 100.0 6.5E-59 1.4E-63 464.6 21.6 302 1-346 159-477 (493)
2 KOG0010 Ubiquitin-like protein 99.1 2.3E-10 4.9E-15 116.2 11.0 80 202-285 153-236 (493)
3 smart00727 STI1 Heat shock cha 97.6 8.2E-05 1.8E-09 51.4 3.5 36 208-243 4-39 (41)
4 smart00727 STI1 Heat shock cha 97.1 0.00041 8.9E-09 47.9 2.6 32 2-33 5-40 (41)
5 TIGR00601 rad23 UV excision re 96.3 0.018 4E-07 58.2 9.1 21 317-339 335-355 (378)
6 KOG0011 Nucleotide excision re 96.2 0.024 5.2E-07 56.0 9.0 62 265-333 249-310 (340)
7 PF09280 XPC-binding: XPC-bind 95.4 0.029 6.2E-07 42.4 4.4 40 210-249 3-46 (59)
8 TIGR00601 rad23 UV excision re 91.7 0.27 5.8E-06 49.9 5.2 21 265-285 281-301 (378)
9 PF09280 XPC-binding: XPC-bind 89.7 0.73 1.6E-05 34.8 4.7 18 2-19 2-23 (59)
10 KOG0011 Nucleotide excision re 87.2 0.94 2E-05 45.1 4.9 51 208-264 216-268 (340)
11 PF00627 UBA: UBA/TS-N domain; 86.4 0.16 3.4E-06 34.3 -0.7 20 321-340 2-21 (37)
12 smart00165 UBA Ubiquitin assoc 85.3 0.29 6.3E-06 32.6 0.3 23 321-343 1-23 (37)
13 cd00194 UBA Ubiquitin Associat 74.1 1.1 2.5E-05 29.8 0.2 20 321-340 1-20 (38)
14 KOG2857 Predicted MYND Zn-fing 26.4 2E+02 0.0043 25.8 5.9 57 14-81 84-140 (157)
15 PF05952 ComX: Bacillus compet 25.1 70 0.0015 24.1 2.5 25 217-241 2-26 (57)
16 PF11445 DUF2894: Protein of u 22.2 1.1E+02 0.0023 28.7 3.7 56 24-80 140-197 (200)
17 KOG2666 UDP-glucose/GDP-mannos 20.8 36 0.00079 34.5 0.3 42 42-93 151-197 (481)
No 1
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=100.00 E-value=6.5e-59 Score=464.57 Aligned_cols=302 Identities=42% Similarity=0.666 Sum_probs=231.4
Q ss_pred ChhhhCCHHHHHhhcCHHHHHHHHhcCHHHHHHHhhChhhhhccCChHHHHHHHHHhcCHHHHHHHHhhhhHHHhhccCC
Q 018937 1 MREIMNMPVVQNLMNNPEIMRNLIMNNPQMREIIDRNPELAHILNDPSTLRQTLEAARNPELMREMMRNTDRAMSNIESS 80 (348)
Q Consensus 1 ~~~mm~nP~~Q~lm~NPe~m~~~i~~nP~mq~l~~~nPel~~~ln~P~~lrq~me~~~NP~~~qEmmr~~dral~~le~~ 80 (348)
+++||+||+||.||+|||+||++|++||+||++|++|||++|++++|+.+||++|++|||+++||+||++||+++++|+|
T Consensus 159 ~~~~m~nP~vq~ll~Npd~mrq~I~anPqmq~lm~~npei~h~ln~p~i~rQtle~arNP~m~qemmrn~d~a~Snlesi 238 (493)
T KOG0010|consen 159 LRQMMENPIVQSLLNNPDLMRQLIMANPQMQDLMQRNPEIGHLLNNPLILRQTLESARNPEMMQEMMRNQDRAMSNLESI 238 (493)
T ss_pred HHHhhhChHHHHHhcChHHHHHHHhcCHHHHHHHhhCCcchhhhcChHHHHHHHHhccCHHHHHHHHhhccccccChhcC
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccchhhHHhhhccchhhhhhhccCCCCCCCCCCchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 018937 81 PEGFNMLRRMYETVQEPFLNATSMAGNAGNDNSNPFAALLGTQGGNQAREGSNNPSTTTSESTTGSPAPNTNPLPNPWMA 160 (348)
Q Consensus 81 PgG~n~lr~~~~diq~pm~na~~~~~~~~~~~~npf~~l~~~~~~~~~~~~~~~~~~~~s~~t~~~~~en~~PLPNPwa~ 160 (348)
|||||++|++|+||+|||+|+... .+++|||++|.+.++... .+++++ ||++|+||||+.
T Consensus 239 PgG~n~l~~my~diqdPm~Na~~~-----~~g~Npfasl~~~~~s~~--------------~~~~~~-eN~~plPn~~~~ 298 (493)
T KOG0010|consen 239 PGGYNALRRMYTDIQDPMLNAASE-----QFGGNPFASLPGNQGSGT--------------GGSPSP-ENNSPLPNPWAQ 298 (493)
T ss_pred ccHHHHHHHHhhhccchhhhhccc-----ccCCCCcccccCccccCC--------------CCCCCc-ccCCCCCCcccC
Confidence 999999999999999999999885 389999999988777521 111234 999999999985
Q ss_pred CCCCCCCCCcccCCCCCCCCCCC-CCCCCCCCCCCcccccCC-CCChHHHHhccCChHHHHHHHHhhCChHHHHHHhhCC
Q 018937 161 AGTGGAQTNTTRSSSLGDARPQT-PAGIAGLSSPGFEDIFGA-MQDTNSLNQMLQNPAVTQMMQSLLSNPQYMNQILGLN 238 (348)
Q Consensus 161 ~g~~~~~~~~~~~~~~s~~~~~~-~~g~~g~g~~~~~~~~g~-~~~p~~m~~mm~nP~~~~mmq~l~sNP~lm~qmi~~n 238 (348)
+........... ..+++.+.+. ....+.++.++..+..+. ..++.++++|++ |+++++++.+.+||.++.+
T Consensus 299 ~~~~s~~a~~~~-~~t~G~~s~~~~~n~s~~~~~~~~a~lq~i~~n~~~~~~l~s-~~~~~m~~~~s~~P~~a~~----- 371 (493)
T KOG0010|consen 299 ASTTSSPAANPT-PGTSGGTSSNGNSNPSQLGSPGMQAGLQMITENPSLLQQLLS-PYIRSMFQSASQNPLQAAQ----- 371 (493)
T ss_pred CCCCCCCCCCCC-cCccCccccCCCCCccccCCcchhhhhhccccChhhhhhccc-hhhHHHHhhhccCchhhhc-----
Confidence 322111100000 0011100000 000001222222222332 478899999999 9999999999999998876
Q ss_pred hhHHHHhhhChHHHHhhcChHHHHhhcCHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCcc-hh-----
Q 018937 239 PQLRSMVDSNSQLREMIQNPEFLRQLTNPETMQQMVTLQQFLLTQLGRAQSTQQPGQTGGGTGIGFIHPYCF-SL----- 312 (348)
Q Consensus 239 P~l~~m~~~nPql~~~mqnP~~l~~m~NP~~mqammqiqqgm~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~-s~----- 312 (348)
+|+ |+||+++++|+||++|++++||||++.+ +.++.+++..+..|..++ ....|..+ .+
T Consensus 372 ------------~~~-mq~p~~~~~~~np~a~~ai~qiqq~~~~-~~~~a~~l~~~~s~~~~~-~n~~p~~~~~~~~~~~ 436 (493)
T KOG0010|consen 372 ------------LRQ-MQNPDVLRAMSNPRAMQAIRQIQQGLQT-LAREAPGLVPGQSGASGP-INGSPTLLMQLFGSLM 436 (493)
T ss_pred ------------ccc-ccCchHhhhhcChHHHHHHHHHHHHHHH-HHhhccccccccccccCC-CCCCchhhhhhhhhhh
Confidence 235 7899999999999999999999999997 789999988865443222 11111111 00
Q ss_pred --------hh-hchHHHHHHHHHhhccCCCCCchhhhhccccc
Q 018937 313 --------FF-LLLELFFTTILKMLKPNGIPYRSFIASVEHLS 346 (348)
Q Consensus 313 --------~~-~~~e~~y~~qL~qL~~mGf~~~~~~~~~~~~~ 346 (348)
.. .-||++|++|||||++|||.| +++||+||-
T Consensus 437 ~~~~~~~n~~~~~pe~r~q~QLeQL~~MGF~n--re~nlqAL~ 477 (493)
T KOG0010|consen 437 LQGLRGSNQQTVPPEERYQTQLEQLNDMGFLD--REANLQALR 477 (493)
T ss_pred hhhccccCcCCCCchHHHHHHHHHHHhcCCcc--HHHHHHHHH
Confidence 01 128999999999999999999 889999873
No 2
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=99.14 E-value=2.3e-10 Score=116.25 Aligned_cols=80 Identities=39% Similarity=0.678 Sum_probs=72.9
Q ss_pred CCChHHHHhccCChHHHHHHHHhhCChHHHHHHhhCChhHHHHhhhChHHHHhhcChHHHHh----hcCHHHHHHHHHHH
Q 018937 202 MQDTNSLNQMLQNPAVTQMMQSLLSNPQYMNQILGLNPQLRSMVDSNSQLREMIQNPEFLRQ----LTNPETMQQMVTLQ 277 (348)
Q Consensus 202 ~~~p~~m~~mm~nP~~~~mmq~l~sNP~lm~qmi~~nP~l~~m~~~nPql~~~mqnP~~l~~----m~NP~~mqammqiq 277 (348)
..+|+.+.+||+||.+ |.|++||+||+++|..||++++++++||+++|+++||+++|+ .+||+.+|++|+++
T Consensus 153 ~snpe~~~~~m~nP~v----q~ll~Npd~mrq~I~anPqmq~lm~~npei~h~ln~p~i~rQtle~arNP~m~qemmrn~ 228 (493)
T KOG0010|consen 153 LSNPEALRQMMENPIV----QSLLNNPDLMRQLIMANPQMQDLMQRNPEIGHLLNNPLILRQTLESARNPEMMQEMMRNQ 228 (493)
T ss_pred ccCHHHHHHhhhChHH----HHHhcChHHHHHHHhcCHHHHHHHhhCCcchhhhcChHHHHHHHHhccCHHHHHHHHhhc
Confidence 4799999999999975 677799999999999999999999999999999999999999 47999999999999
Q ss_pred HHHHHhhc
Q 018937 278 QFLLTQLG 285 (348)
Q Consensus 278 qgm~~~l~ 285 (348)
+...++++
T Consensus 229 d~a~Snle 236 (493)
T KOG0010|consen 229 DRAMSNLE 236 (493)
T ss_pred cccccChh
Confidence 87666554
No 3
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=97.57 E-value=8.2e-05 Score=51.41 Aligned_cols=36 Identities=39% Similarity=0.621 Sum_probs=31.6
Q ss_pred HHhccCChHHHHHHHHhhCChHHHHHHhhCChhHHH
Q 018937 208 LNQMLQNPAVTQMMQSLLSNPQYMNQILGLNPQLRS 243 (348)
Q Consensus 208 m~~mm~nP~~~~mmq~l~sNP~lm~qmi~~nP~l~~ 243 (348)
+.++++||+++++++.+++||++++.++.+||++++
T Consensus 4 ~~~~l~~P~~~~~l~~~~~nP~~~~~~~~~nP~~~~ 39 (41)
T smart00727 4 MALRLQNPQVQSLLQDMQQNPDMLAQMLQENPQLLQ 39 (41)
T ss_pred HHHHHcCHHHHHHHHHHHHCHHHHHHHHHhCHHhHh
Confidence 456778999999999999999999999977888764
No 4
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=97.09 E-value=0.00041 Score=47.87 Aligned_cols=32 Identities=28% Similarity=0.629 Sum_probs=22.4
Q ss_pred hhhhCCHHHHHhhc----CHHHHHHHHhcCHHHHHH
Q 018937 2 REIMNMPVVQNLMN----NPEIMRNLIMNNPQMREI 33 (348)
Q Consensus 2 ~~mm~nP~~Q~lm~----NPe~m~~~i~~nP~mq~l 33 (348)
.++++||.|+.+++ ||++++.++++||++++.
T Consensus 5 ~~~l~~P~~~~~l~~~~~nP~~~~~~~~~nP~~~~~ 40 (41)
T smart00727 5 ALRLQNPQVQSLLQDMQQNPDMLAQMLQENPQLLQL 40 (41)
T ss_pred HHHHcCHHHHHHHHHHHHCHHHHHHHHHhCHHhHhh
Confidence 46677787777665 787777777667776643
No 5
>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=96.32 E-value=0.018 Score=58.22 Aligned_cols=21 Identities=19% Similarity=0.022 Sum_probs=16.0
Q ss_pred hHHHHHHHHHhhccCCCCCchhh
Q 018937 317 LELFFTTILKMLKPNGIPYRSFI 339 (348)
Q Consensus 317 ~e~~y~~qL~qL~~mGf~~~~~~ 339 (348)
+|++ +-+++|+++||.-+..|
T Consensus 335 ~eE~--~AIeRL~~LGF~r~~vi 355 (378)
T TIGR00601 335 PEEK--EAIERLCALGFDRGLVI 355 (378)
T ss_pred HHHH--HHHHHHHHcCCCHHHHH
Confidence 4554 67999999999766554
No 6
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=96.22 E-value=0.024 Score=56.05 Aligned_cols=62 Identities=18% Similarity=0.133 Sum_probs=31.6
Q ss_pred cCHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCcchhhhhchHHHHHHHHHhhccCCC
Q 018937 265 TNPETMQQMVTLQQFLLTQLGRAQSTQQPGQTGGGTGIGFIHPYCFSLFFLLLELFFTTILKMLKPNGI 333 (348)
Q Consensus 265 ~NP~~mqammqiqqgm~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~s~~~~~~e~~y~~qL~qL~~mGf 333 (348)
.||+.+|.+.+-|..+...|+..+-+ +.+.+.+.....+..+ -...-||+. +-+++||+|||
T Consensus 249 ~nP~L~q~Iq~nqe~Fl~mlnep~~~-~~~~~~~~~~~~~~~~----~I~vtpee~--eAIeRL~alGF 310 (340)
T KOG0011|consen 249 QNPQLLQLIQENQEAFLQLLNEPVEG-GDGGGTGAPAAEGPGH----QIQVTPEEK--EAIERLEALGF 310 (340)
T ss_pred hCHHHHHHHHHHHHHHHHHhhccccc-ccccccccccccCCcc----eEecCHHHH--HHHHHHHHhCC
Confidence 46666777777777777766544443 1111111111111101 111125664 56899999999
No 7
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=95.36 E-value=0.029 Score=42.38 Aligned_cols=40 Identities=33% Similarity=0.514 Sum_probs=23.8
Q ss_pred hccCChHHHHHHHHhhCChHHHHHHh----hCChhHHHHhhhCh
Q 018937 210 QMLQNPAVTQMMQSLLSNPQYMNQIL----GLNPQLRSMVDSNS 249 (348)
Q Consensus 210 ~mm~nP~~~~mmq~l~sNP~lm~qmi----~~nP~l~~m~~~nP 249 (348)
.+.++|.+.++-+.+.+||+++..++ ..||++.+++.+||
T Consensus 3 ~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~ 46 (59)
T PF09280_consen 3 FLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNP 46 (59)
T ss_dssp GGTTSHHHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTH
T ss_pred HHHcChHHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCH
Confidence 46778888888888888887554443 34444444433333
No 8
>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=91.71 E-value=0.27 Score=49.89 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=11.4
Q ss_pred cCHHHHHHHHHHHHHHHHhhc
Q 018937 265 TNPETMQQMVTLQQFLLTQLG 285 (348)
Q Consensus 265 ~NP~~mqammqiqqgm~~~l~ 285 (348)
+||+.+|.+.+-+..+...|+
T Consensus 281 ~nP~l~q~I~~n~e~Fl~ll~ 301 (378)
T TIGR00601 281 ENPQLLQQISQHPEQFLQMLN 301 (378)
T ss_pred hCHHHHHHHHHCHHHHHHHhc
Confidence 455555555555555555443
No 9
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=89.66 E-value=0.73 Score=34.78 Aligned_cols=18 Identities=33% Similarity=0.527 Sum_probs=9.6
Q ss_pred hhhhCCHHHHHh----hcCHHH
Q 018937 2 REIMNMPVVQNL----MNNPEI 19 (348)
Q Consensus 2 ~~mm~nP~~Q~l----m~NPe~ 19 (348)
..+.++|.|+.| -.||++
T Consensus 2 ~~Lr~~Pqf~~lR~~vq~NP~l 23 (59)
T PF09280_consen 2 EFLRNNPQFQQLRQLVQQNPQL 23 (59)
T ss_dssp GGGTTSHHHHHHHHHHHC-GGG
T ss_pred hHHHcChHHHHHHHHHHHCHHH
Confidence 456777766543 256543
No 10
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=87.18 E-value=0.94 Score=45.08 Aligned_cols=51 Identities=33% Similarity=0.562 Sum_probs=36.5
Q ss_pred HHhccCChHHHHHHHHhhCChHHHHHHhhCChhHHHHhhhChHHHHhhc-ChH-HHHhh
Q 018937 208 LNQMLQNPAVTQMMQSLLSNPQYMNQILGLNPQLRSMVDSNSQLREMIQ-NPE-FLRQL 264 (348)
Q Consensus 208 m~~mm~nP~~~~mmq~l~sNP~lm~qmi~~nP~l~~m~~~nPql~~~mq-nP~-~l~~m 264 (348)
+.-+.+.|.++++.+-+.+||++++-|+ +++-+.||++++.++ |++ |++++
T Consensus 216 l~fLr~~~qf~~lR~~iqqNP~ll~~~L------qqlg~~nP~L~q~Iq~nqe~Fl~ml 268 (340)
T KOG0011|consen 216 LEFLRNQPQFQQLRQMIQQNPELLHPLL------QQLGKQNPQLLQLIQENQEAFLQLL 268 (340)
T ss_pred hhhhhccHHHHHHHHHHhhCHHHHHHHH------HHHhhhCHHHHHHHHHHHHHHHHHh
Confidence 4567889999999999999999986554 566667777776653 443 44444
No 11
>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=86.38 E-value=0.16 Score=34.27 Aligned_cols=20 Identities=10% Similarity=-0.039 Sum_probs=15.7
Q ss_pred HHHHHHhhccCCCCCchhhh
Q 018937 321 FTTILKMLKPNGIPYRSFIA 340 (348)
Q Consensus 321 y~~qL~qL~~mGf~~~~~~~ 340 (348)
|.+.|++|.+|||..++..+
T Consensus 2 ~~~~v~~L~~mGf~~~~~~~ 21 (37)
T PF00627_consen 2 DEEKVQQLMEMGFSREQARE 21 (37)
T ss_dssp HHHHHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHH
Confidence 67899999999999865544
No 12
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=85.34 E-value=0.29 Score=32.57 Aligned_cols=23 Identities=9% Similarity=0.073 Sum_probs=17.8
Q ss_pred HHHHHHhhccCCCCCchhhhhcc
Q 018937 321 FTTILKMLKPNGIPYRSFIASVE 343 (348)
Q Consensus 321 y~~qL~qL~~mGf~~~~~~~~~~ 343 (348)
|.+.+++|.+|||..++..+.++
T Consensus 1 ~~~~v~~L~~mGf~~~~a~~aL~ 23 (37)
T smart00165 1 DEEKIDQLLEMGFSREEALKALR 23 (37)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHH
Confidence 46789999999999876655443
No 13
>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=74.10 E-value=1.1 Score=29.76 Aligned_cols=20 Identities=15% Similarity=-0.026 Sum_probs=15.4
Q ss_pred HHHHHHhhccCCCCCchhhh
Q 018937 321 FTTILKMLKPNGIPYRSFIA 340 (348)
Q Consensus 321 y~~qL~qL~~mGf~~~~~~~ 340 (348)
|.+.+++|.+|||...+.++
T Consensus 1 ~~~~v~~L~~mGf~~~~~~~ 20 (38)
T cd00194 1 DEEKLEQLLEMGFSREEARK 20 (38)
T ss_pred CHHHHHHHHHcCCCHHHHHH
Confidence 46789999999999644443
No 14
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=26.44 E-value=2e+02 Score=25.80 Aligned_cols=57 Identities=23% Similarity=0.512 Sum_probs=35.7
Q ss_pred hcCHHHHHHHHhcCHHHHHHHhhChhhhhccCChHHHHHHHHHhcCHHHHHHHHhhhhHHHhhccCCC
Q 018937 14 MNNPEIMRNLIMNNPQMREIIDRNPELAHILNDPSTLRQTLEAARNPELMREMMRNTDRAMSNIESSP 81 (348)
Q Consensus 14 m~NPe~m~~~i~~nP~mq~l~~~nPel~~~ln~P~~lrq~me~~~NP~~~qEmmr~~dral~~le~~P 81 (348)
+.+-..+|.+| .||.+|+||+.+-+..+++ ..+.++++-|.. ..-.|--++++|-.|
T Consensus 84 l~ssseLrsll-~dp~Lr~Li~sid~~~n~~------kel~aamqeelf----vefadailq~ve~s~ 140 (157)
T KOG2857|consen 84 LPSSSELRSLL-EDPHLRNLIESIDELLNIM------KELVAAMQEELF----VEFADAILQQVEPSP 140 (157)
T ss_pred ccchHHHHHHH-hCHHHHHHHHHHHHHhhHH------HHHHHHhcchHH----HHHHHHHHHhhcCCC
Confidence 34556789998 8899999998887777643 344444555522 234455555555444
No 15
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=25.08 E-value=70 Score=24.14 Aligned_cols=25 Identities=16% Similarity=0.361 Sum_probs=20.1
Q ss_pred HHHHHHHhhCChHHHHHHhhCChhH
Q 018937 217 VTQMMQSLLSNPQYMNQILGLNPQL 241 (348)
Q Consensus 217 ~~~mmq~l~sNP~lm~qmi~~nP~l 241 (348)
+|.+++-|.+||+++.++...+--+
T Consensus 2 ~Q~iV~YLv~nPevl~kl~~g~asL 26 (57)
T PF05952_consen 2 KQEIVNYLVQNPEVLEKLKEGEASL 26 (57)
T ss_pred hHHHHHHHHHChHHHHHHHcCCeeE
Confidence 4778899999999999998665544
No 16
>PF11445 DUF2894: Protein of unknown function (DUF2894); InterPro: IPR021549 This is a bacterial family of uncharacterised proteins.
Probab=22.21 E-value=1.1e+02 Score=28.72 Aligned_cols=56 Identities=23% Similarity=0.414 Sum_probs=47.7
Q ss_pred HhcCHHHHHHHhhChhhhhccCChHHHHHHHHHhcC--HHHHHHHHhhhhHHHhhccCC
Q 018937 24 IMNNPQMREIIDRNPELAHILNDPSTLRQTLEAARN--PELMREMMRNTDRAMSNIESS 80 (348)
Q Consensus 24 i~~nP~mq~l~~~nPel~~~ln~P~~lrq~me~~~N--P~~~qEmmr~~dral~~le~~ 80 (348)
+...-+|++-+++.||=.-.||+..++-..+.++|. |++++.++.-.| +|.+||-+
T Consensus 140 ~~~e~qlrqsl~qvP~nAGPLNS~~LVhRsL~lMrelSP~YL~~FlsYvD-tL~WLEq~ 197 (200)
T PF11445_consen 140 VSAEQQLRQSLEQVPENAGPLNSHRLVHRSLSLMRELSPGYLQQFLSYVD-TLSWLEQL 197 (200)
T ss_pred hhHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHH-HHHHHHHh
Confidence 455678888899999999999999999999999986 999999998775 67777654
No 17
>KOG2666 consensus UDP-glucose/GDP-mannose dehydrogenase [Carbohydrate transport and metabolism; Signal transduction mechanisms]
Probab=20.80 E-value=36 Score=34.48 Aligned_cols=42 Identities=33% Similarity=0.661 Sum_probs=31.2
Q ss_pred hccCChHHHHH--HHHHhcCHHHHHHHHhhhhHHHhhccCCCccchh---hHHhhhc
Q 018937 42 HILNDPSTLRQ--TLEAARNPELMREMMRNTDRAMSNIESSPEGFNM---LRRMYET 93 (348)
Q Consensus 42 ~~ln~P~~lrq--~me~~~NP~~~qEmmr~~dral~~le~~PgG~n~---lr~~~~d 93 (348)
++|+|||+|.+ +++- +-|.||-|-+=+.+|+|+.| |+.+|..
T Consensus 151 qilsnpeflaegtaikd----------l~npdrvligg~etpeg~~av~~l~~vyeh 197 (481)
T KOG2666|consen 151 QILSNPEFLAEGTAIKD----------LFNPDRVLIGGRETPEGFQAVQALKDVYEH 197 (481)
T ss_pred EeccChHHhcccchhhh----------hcCCceEEECCCCChhHHHHHHHHHHHHHh
Confidence 46777777765 3322 34668889999999999977 6888877
Done!