Query 015358
Match_columns 408
No_of_seqs 156 out of 455
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:33:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015358.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015358hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08590 DUF1771: Domain of un 99.5 1.9E-15 4E-20 118.6 1.4 66 235-300 1-66 (66)
2 PF01713 Smr: Smr domain; Int 99.3 2.2E-12 4.7E-17 103.9 6.4 55 307-406 1-55 (83)
3 smart00463 SMR Small MutS-rela 99.3 2.4E-12 5.1E-17 103.0 6.5 62 304-408 1-63 (80)
4 COG2840 Uncharacterized protei 98.4 4.3E-07 9.4E-12 85.1 6.8 60 303-407 95-155 (184)
5 KOG2401 Predicted MutS-related 98.2 1E-06 2.3E-11 91.5 4.2 383 1-405 14-420 (448)
6 PRK04946 hypothetical protein; 98.0 6.6E-06 1.4E-10 77.0 5.3 56 303-407 94-149 (181)
7 PRK00409 recombination and DNA 97.2 0.00039 8.5E-09 77.4 5.6 55 304-407 704-758 (782)
8 PF02845 CUE: CUE domain; Int 97.1 0.0011 2.4E-08 47.7 5.3 40 96-135 2-41 (42)
9 TIGR01069 mutS2 MutS2 family p 97.0 0.001 2.2E-08 74.1 5.7 55 304-407 693-747 (771)
10 smart00546 CUE Domain that may 96.6 0.0043 9.3E-08 44.7 4.8 40 96-135 3-42 (43)
11 PF00627 UBA: UBA/TS-N domain; 93.1 0.26 5.6E-06 34.4 5.0 36 95-132 2-37 (37)
12 cd00194 UBA Ubiquitin Associat 86.5 1.7 3.6E-05 30.0 4.6 35 97-133 3-37 (38)
13 smart00165 UBA Ubiquitin assoc 86.2 1.7 3.8E-05 29.8 4.5 35 96-132 2-36 (37)
14 PF03474 DMA: DMRTA motif; In 81.7 3.1 6.7E-05 30.5 4.3 35 98-132 4-38 (39)
15 COG1193 Mismatch repair ATPase 75.8 4.4 9.6E-05 45.9 5.4 55 304-407 676-730 (753)
16 PF14346 DUF4398: Domain of un 65.5 52 0.0011 27.5 8.5 43 245-287 40-82 (103)
17 PF04505 Dispanin: Interferon- 65.2 8.4 0.00018 31.8 3.6 31 252-282 39-69 (82)
18 PF13763 DUF4167: Domain of un 56.2 49 0.0011 27.9 6.5 39 250-288 39-77 (80)
19 smart00685 DM14 Repeats in fly 50.4 61 0.0013 25.7 5.9 39 247-285 4-43 (59)
20 KOG4588 Predicted ubiquitin-co 45.2 23 0.0005 35.3 3.5 33 105-137 1-33 (267)
21 TIGR00601 rad23 UV excision re 44.2 31 0.00067 36.2 4.5 39 95-135 337-375 (378)
22 COG2250 Uncharacterized conser 42.5 98 0.0021 27.6 6.8 41 240-280 3-43 (132)
23 PF03357 Snf7: Snf7; InterPro 41.0 1.6E+02 0.0034 26.0 7.9 55 237-291 11-65 (171)
24 PF02954 HTH_8: Bacterial regu 40.1 33 0.00071 24.5 2.8 26 109-134 5-30 (42)
25 COG2178 Predicted RNA-binding 34.8 2.1E+02 0.0045 28.0 8.1 51 234-284 13-63 (204)
26 PF14555 UBA_4: UBA-like domai 21.7 2.3E+02 0.005 20.3 4.6 34 98-132 3-36 (43)
No 1
>PF08590 DUF1771: Domain of unknown function (DUF1771); InterPro: IPR013899 This domain is almost always found adjacent to IPR002625 from INTERPRO. ; PDB: 2VKC_A.
Probab=99.53 E-value=1.9e-15 Score=118.56 Aligned_cols=66 Identities=27% Similarity=0.295 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 015358 235 VYLVHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAAKEILGIRNS 300 (408)
Q Consensus 235 ~Y~~~RkeA~~~~r~R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae~an~kAA~~If~~rN~ 300 (408)
+|..+|.+|..+++.|++||++|++||++||+..|++||++|+.|..+|+++|.+||+.||..+|.
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 499999999999999999999999999999999999999999999999999999999999999983
No 2
>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=99.33 E-value=2.2e-12 Score=103.90 Aligned_cols=55 Identities=45% Similarity=0.739 Sum_probs=44.2
Q ss_pred eecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEEEEcc
Q 015358 307 LDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITGI 386 (408)
Q Consensus 307 LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~VITG~ 386 (408)
|||||+++.||+.+|+++|..++.+- ...|.||||+
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~~--------------------------------------------~~~~~II~G~ 36 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQRG--------------------------------------------IRELRIITGK 36 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHTT--------------------------------------------HSEEEEE--S
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHcC--------------------------------------------CCEEEEEecc
Confidence 89999999999999999999986430 1379999999
Q ss_pred CCCCCCCCCcHHHHHHHHHh
Q 015358 387 GNHSRGQAALPTAVKNFLSE 406 (408)
Q Consensus 387 G~HS~G~arL~pAV~~fL~e 406 (408)
|+||.++. |+++|+.||.+
T Consensus 37 G~hS~~g~-Lk~~V~~~L~~ 55 (83)
T PF01713_consen 37 GNHSKGGV-LKRAVRRWLEE 55 (83)
T ss_dssp TCTCCTSH-HHHHHHHHHHH
T ss_pred CCCCCCCc-HHHHHHHHHHh
Confidence 99999665 99999999965
No 3
>smart00463 SMR Small MutS-related domain.
Probab=99.33 E-value=2.4e-12 Score=103.02 Aligned_cols=62 Identities=39% Similarity=0.659 Sum_probs=52.4
Q ss_pred CCceecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEEE
Q 015358 304 MWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVI 383 (408)
Q Consensus 304 ~~~LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~VI 383 (408)
.|+|||||+++.||+.+|+.+|+.++... . ...+.||
T Consensus 1 ~~~lDLHG~~~~eA~~~l~~~l~~~~~~~----------------------------------------~---~~~~~II 37 (80)
T smart00463 1 KWSLDLHGLTVEEALTALDKFLNNARLKG----------------------------------------L---EQKLVII 37 (80)
T ss_pred CCeEEcCCCCHHHHHHHHHHHHHHHHHcC----------------------------------------C---CceEEEE
Confidence 47999999999999999999999986420 0 0369999
Q ss_pred EccCCCCC-CCCCcHHHHHHHHHhcC
Q 015358 384 TGIGNHSR-GQAALPTAVKNFLSESG 408 (408)
Q Consensus 384 TG~G~HS~-G~arL~pAV~~fL~e~G 408 (408)
||+|+||. |.++|+++|.++|...+
T Consensus 38 ~G~G~~s~~g~~~i~~~l~~~l~~~~ 63 (80)
T smart00463 38 TGKGKHSLGGKSGVKPALKEHLRVES 63 (80)
T ss_pred EcccCCCccchhhHHHHHHhchhhcc
Confidence 99999998 77999999999997643
No 4
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.43 E-value=4.3e-07 Score=85.13 Aligned_cols=60 Identities=32% Similarity=0.472 Sum_probs=51.5
Q ss_pred CCCceecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEE
Q 015358 303 DMWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQV 382 (408)
Q Consensus 303 ~~~~LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~V 382 (408)
....|||||+++.||-..|-.+|...... +..++.|
T Consensus 95 ~e~~LDLHG~tq~eAr~~L~~Fi~~a~~~--------------------------------------------~~rcv~V 130 (184)
T COG2840 95 PEARLDLHGLTQEEARQELGAFIARARAE--------------------------------------------GLRCVLV 130 (184)
T ss_pred cceeeeccCCCHHHHHHHHHHHHHHHHHh--------------------------------------------CCcEEEE
Confidence 57899999999999999999999987432 1237999
Q ss_pred EEccCCCCCC-CCCcHHHHHHHHHhc
Q 015358 383 ITGIGNHSRG-QAALPTAVKNFLSES 407 (408)
Q Consensus 383 ITG~G~HS~G-~arL~pAV~~fL~e~ 407 (408)
|||.|. |.| .+.|+..|..||.+.
T Consensus 131 ihGkG~-s~g~~~vLK~~Vp~WL~qh 155 (184)
T COG2840 131 IHGKGR-SKGSKPVLKSQVPRWLTQH 155 (184)
T ss_pred EeCCCc-CCCCchhHHHHHHHHHHhC
Confidence 999999 998 589999999999863
No 5
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=98.20 E-value=1e-06 Score=91.47 Aligned_cols=383 Identities=15% Similarity=0.059 Sum_probs=199.7
Q ss_pred CCCCCCCCCCchhhhHHHHhhcCCCCCCCCCCCCCCCccccCCc-cccccccCCCCccCCcccccccCCCCCCccccccc
Q 015358 1 MSLTRVKSPGWAAFDLKQRQKQGLAPETDKDSYPPISSTLTSLR-NCENVSRNTDVLVKPFSSVLRPSVEFPTLTEENEC 79 (408)
Q Consensus 1 m~~~~~~~~gw~afd~k~r~~~~~~~e~d~d~fp~~~~~~~~~~-~~~~~~~~~~~~~k~f~sv~~p~~~f~~~~~~~~~ 79 (408)
|||+.....+|..|.+..+++...+.....|++|++.+.-...- -|.-+-.+..+....+++++.++..+++..+..+|
T Consensus 14 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~ 93 (448)
T KOG2401|consen 14 MSLTLSLAAFSFSFKLVDLKAASEESSDEVDLGPPELSEMATSTSSADRLQYTIELLEPSPSSVSFESLRARASDENVDR 93 (448)
T ss_pred ccchhccchhhhhhhhHhhhhcccccccccccCCCcchhhccccchhhhhcccccccCCCcccccccccccchhhhcccc
Confidence 78999999999999999999999999999999999988753333 23333356666888999999999999999999999
Q ss_pred cccCCCC-------CccccccchHHHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHHHhhhccCCCcccccccccCC
Q 015358 80 DYKGKHG-------HKAIEQHSRDLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGMVSSSGSAEENKETKIAE 152 (408)
Q Consensus 80 ~~~~~~~-------~~~~~~~~~~~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L~~m~~~~~~~~~~~~~~~~~ 152 (408)
++.+.-+ .....++....++.....+..|.....|.+..-.....+-....++..+.. .+..+......+..
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~f~~~~~~-~~~~~~~~~~~~~~ 172 (448)
T KOG2401|consen 94 GNQERILDRSRNQVAGKLKVSFVEKKLNEEEPQKEINPDGRILPEDPSFEESFRVENGFDPGEAI-AFKIEDLPQKQVEG 172 (448)
T ss_pred HHHHhhcccccccccccccccccccccCccccccccCCcccccccccchHHHHHHhccCccchhh-hcchhhhccccccc
Confidence 9998111 122223445566666666677766666555444333333333333332222 11111111001111
Q ss_pred CCCCCCCCcccccCCchhhhhhhhhccccccccCCCcccCCcccccccccccccCCCcccchhhhhhhcCCCCCCCCccC
Q 015358 153 SSSTIDESPCYRKGGEICFLEKALDLSNLSTTTGDGVNDNFIESVDVRASSVINVSDKDDGMKSIMERLSSLPIEPEWEE 232 (408)
Q Consensus 153 ~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~s~~~~~~~~~~~~~~~~~~~sip~epewee 232 (408)
+-. ++++.. .+ ....-++.......+++.+ ....+.... .. +-+.......+..-.|..
T Consensus 173 ~~~--~n~~~~---~~--~~~~~d~~~~~~~~~~~~~-----------~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~~ 231 (448)
T KOG2401|consen 173 EDV--DNCKVK---NQ--ITNSSDSKMATEPGLNDSL-----------KKAYENVDS-SE--ESVELLRKEGFSVDVPSN 231 (448)
T ss_pred ccc--ccceee---cc--ccccccccccccccccchh-----------hccccccCc-ch--hhhhhhccCCCCccCcch
Confidence 100 000000 00 0000011111111122211 111110000 00 000001111111111111
Q ss_pred --------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 015358 233 --------DDVYLVHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAAKEILGIRNSENDM 304 (408)
Q Consensus 233 --------d~~Y~~~RkeA~~~~r~R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae~an~kAA~~If~~rN~~~~~ 304 (408)
...|...+.........+..++....-|+.-+.......++.+.+......+..+.++....|...+.....
T Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~s~~~~ 311 (448)
T KOG2401|consen 232 AEKNSAKRLEELQKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNKESIKSE 311 (448)
T ss_pred hhcccccchhhcchhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhhhhhhhh
Confidence 233445555555555666666666667776666677777777777777777777777777776666666666
Q ss_pred CceecCCCCHHHHHHHHHHHHHHHHhh------CCCCCCCCC-ccccccCC-cccccccccccccchhhhhhhhhhhhcc
Q 015358 305 WKLDLHGLHAAEAVQALQERLQKIEMQ------RPMNCSVSP-KKVKSKNG-MVCTASLESFGCMDMEVVDKQRSSLRQI 376 (408)
Q Consensus 305 ~~LDLHGLhv~EAv~iL~e~L~~i~~q------l~~~rs~sp-~~~~~~~g-~~~s~~~~~~~~~d~~~~~~q~~~~r~~ 376 (408)
..+|.|++.+..+.+.++..+...... ..+.+.... .+..+.++ ......-+.+..+...+..++.+.....
T Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~r~~~~~~~~~~i~~~~~ 391 (448)
T KOG2401|consen 312 REIDNQRLYKKAAEQKAQPEIEDAINLQASELKPKVSLAVKGSYAVAKLKPATQWKLDNEEIERRSEVGEHGEKISELSR 391 (448)
T ss_pred HHhhhhhHHHHHHHhhhhhhhhhhhhhhhhhhchhhhhcccccchhhhcchHHHHHHhhhhhhcccccccchhhhHhHhh
Confidence 677777766666655555444332100 000000000 00000011 0111111222333333444444445555
Q ss_pred CccEEEEEccCCCCCCCCCcHHHHHHHHH
Q 015358 377 QKSLQVITGIGNHSRGQAALPTAVKNFLS 405 (408)
Q Consensus 377 ~~~L~VITG~G~HS~G~arL~pAV~~fL~ 405 (408)
...+.|++|+|.||.+.+++++++...+.
T Consensus 392 ~~~~qv~~~~~~~s~~~~~~~~~~~~~~~ 420 (448)
T KOG2401|consen 392 RLKLQVLFGRGIHSRGEARLPRAEKRSYE 420 (448)
T ss_pred hccccccccccccCccchhhhhhhhhhcc
Confidence 56789999999999999988888776544
No 6
>PRK04946 hypothetical protein; Provisional
Probab=98.03 E-value=6.6e-06 Score=76.98 Aligned_cols=56 Identities=25% Similarity=0.262 Sum_probs=46.8
Q ss_pred CCCceecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEE
Q 015358 303 DMWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQV 382 (408)
Q Consensus 303 ~~~~LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~V 382 (408)
....|||||+++.||...|.++|...... +...+.|
T Consensus 94 ~~~~LDLhG~~~eeA~~~L~~fl~~a~~~--------------------------------------------g~r~v~I 129 (181)
T PRK04946 94 PELFLDLHGLTQLQAKQELGALIAACRKE--------------------------------------------HVFCACV 129 (181)
T ss_pred CceEEECCCCCHHHHHHHHHHHHHHHHHc--------------------------------------------CCCEEEE
Confidence 46799999999999999999999986421 1237999
Q ss_pred EEccCCCCCCCCCcHHHHHHHHHhc
Q 015358 383 ITGIGNHSRGQAALPTAVKNFLSES 407 (408)
Q Consensus 383 ITG~G~HS~G~arL~pAV~~fL~e~ 407 (408)
|+|+|. +.|+..|..||.+.
T Consensus 130 IHGkG~-----gvLk~~V~~wL~q~ 149 (181)
T PRK04946 130 MHGHGK-----HILKQQTPLWLAQH 149 (181)
T ss_pred EcCCCH-----hHHHHHHHHHHcCC
Confidence 999985 69999999999753
No 7
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=97.23 E-value=0.00039 Score=77.40 Aligned_cols=55 Identities=27% Similarity=0.431 Sum_probs=45.8
Q ss_pred CCceecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEEE
Q 015358 304 MWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVI 383 (408)
Q Consensus 304 ~~~LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~VI 383 (408)
..+|||||+++.||+..|+.+|..... .+...++||
T Consensus 704 ~~~lDL~G~~~eeA~~~l~~fl~~a~~--------------------------------------------~g~~~v~II 739 (782)
T PRK00409 704 SLELDLRGMRYEEALERLDKYLDDALL--------------------------------------------AGYGEVLII 739 (782)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHH--------------------------------------------cCCCEEEEE
Confidence 568999999999999999999998532 122479999
Q ss_pred EccCCCCCCCCCcHHHHHHHHHhc
Q 015358 384 TGIGNHSRGQAALPTAVKNFLSES 407 (408)
Q Consensus 384 TG~G~HS~G~arL~pAV~~fL~e~ 407 (408)
+|+|. ..|+.+|..||.++
T Consensus 740 HGkGt-----G~Lr~~v~~~L~~~ 758 (782)
T PRK00409 740 HGKGT-----GKLRKGVQEFLKKH 758 (782)
T ss_pred cCCCh-----hHHHHHHHHHHcCC
Confidence 99974 59999999999864
No 8
>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=97.13 E-value=0.0011 Score=47.70 Aligned_cols=40 Identities=23% Similarity=0.371 Sum_probs=35.9
Q ss_pred HHHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHHHhh
Q 015358 96 DLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGM 135 (408)
Q Consensus 96 ~~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L~~m 135 (408)
+..++.|++|||-.+.+.|+.+|.+.++|++.|+..|-.|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 3568999999999999999999999999999999988765
No 9
>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=96.96 E-value=0.001 Score=74.09 Aligned_cols=55 Identities=25% Similarity=0.386 Sum_probs=45.6
Q ss_pred CCceecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEEE
Q 015358 304 MWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVI 383 (408)
Q Consensus 304 ~~~LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~VI 383 (408)
...|||||+++.||+..|+.+|..... .+...++||
T Consensus 693 ~~~ldl~G~~~~eA~~~l~~~ld~a~~--------------------------------------------~g~~~v~II 728 (771)
T TIGR01069 693 SLTLDLRGQRSEEALDRLEKFLNDALL--------------------------------------------AGYEVVLII 728 (771)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHH--------------------------------------------CCCCEEEEE
Confidence 458999999999999999999998632 112379999
Q ss_pred EccCCCCCCCCCcHHHHHHHHHhc
Q 015358 384 TGIGNHSRGQAALPTAVKNFLSES 407 (408)
Q Consensus 384 TG~G~HS~G~arL~pAV~~fL~e~ 407 (408)
+|+|. ..|+.+|..||.++
T Consensus 729 HGkGt-----G~Lr~~v~~~L~~~ 747 (771)
T TIGR01069 729 HGKGS-----GKLRKGVQELLKNH 747 (771)
T ss_pred cCCCh-----hHHHHHHHHHhcCC
Confidence 99974 57999999999864
No 10
>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=96.61 E-value=0.0043 Score=44.70 Aligned_cols=40 Identities=28% Similarity=0.339 Sum_probs=36.2
Q ss_pred HHHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHHHhh
Q 015358 96 DLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGM 135 (408)
Q Consensus 96 ~~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L~~m 135 (408)
...++.|++|||-++..+|+.+|.+.+||++.|+..|-.|
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 3468899999999999999999999999999999877654
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=93.09 E-value=0.26 Score=34.45 Aligned_cols=36 Identities=14% Similarity=0.278 Sum_probs=32.0
Q ss_pred hHHHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHH
Q 015358 95 RDLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (408)
Q Consensus 95 ~~~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L 132 (408)
.+-.+++|++| +.+.+.....|.+++||+++|+..|
T Consensus 2 ~~~~v~~L~~m--Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEM--GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHH--TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 35679999999 8999999999999999999999887
No 12
>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=86.54 E-value=1.7 Score=29.99 Aligned_cols=35 Identities=20% Similarity=0.236 Sum_probs=30.9
Q ss_pred HHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHHH
Q 015358 97 LALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLE 133 (408)
Q Consensus 97 ~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L~ 133 (408)
..+++|.+| +.+.+.+..+|.+++||+++|...|-
T Consensus 3 ~~v~~L~~m--Gf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLEM--GFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 478899998 57799999999999999999998873
No 13
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=86.17 E-value=1.7 Score=29.79 Aligned_cols=35 Identities=14% Similarity=0.235 Sum_probs=31.2
Q ss_pred HHHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHH
Q 015358 96 DLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (408)
Q Consensus 96 ~~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L 132 (408)
.-++++|++| +.+.+.+..+|.+++||+++|+..|
T Consensus 2 ~~~v~~L~~m--Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEM--GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 3468899999 7899999999999999999999876
No 14
>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=81.72 E-value=3.1 Score=30.55 Aligned_cols=35 Identities=14% Similarity=0.307 Sum_probs=31.9
Q ss_pred HHHHHHHhccccchHHHHHHHHHhhccHHHHHHHH
Q 015358 98 ALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (408)
Q Consensus 98 ~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L 132 (408)
.++-|...||.-..+.++-||..+++|+-+|.+.+
T Consensus 4 pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 4 PIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHHh
Confidence 46789999999999999999999999999998754
No 15
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=75.76 E-value=4.4 Score=45.87 Aligned_cols=55 Identities=24% Similarity=0.430 Sum_probs=45.4
Q ss_pred CCceecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCccEEEE
Q 015358 304 MWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVI 383 (408)
Q Consensus 304 ~~~LDLHGLhv~EAv~iL~e~L~~i~~ql~~~rs~sp~~~~~~~g~~~s~~~~~~~~~d~~~~~~q~~~~r~~~~~L~VI 383 (408)
...|||+|..+.+|+..|...+..+-. + +...+.||
T Consensus 676 ~~~ldLrg~r~e~a~~~l~k~i~eail----------------~----------------------------~~~~v~ii 711 (753)
T COG1193 676 SNRLDLRGERSEEALDELDKSIDEAIL----------------E----------------------------GYEKVSII 711 (753)
T ss_pred cccccccccccHHHHHHHHhhhHHHHH----------------c----------------------------CCcceeEE
Confidence 469999999999999999999998632 1 12368999
Q ss_pred EccCCCCCCCCCcHHHHHHHHHhc
Q 015358 384 TGIGNHSRGQAALPTAVKNFLSES 407 (408)
Q Consensus 384 TG~G~HS~G~arL~pAV~~fL~e~ 407 (408)
.|. |-.+|+..|.+||.++
T Consensus 712 hgk-----GtG~lre~v~~~Lk~~ 730 (753)
T COG1193 712 HGK-----GTGKLREGVQEYLKKH 730 (753)
T ss_pred eee-----echHHHHHHHHHHHhC
Confidence 998 5578999999999875
No 16
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=65.55 E-value=52 Score=27.51 Aligned_cols=43 Identities=21% Similarity=0.159 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHH
Q 015358 245 KMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLN 287 (408)
Q Consensus 245 ~~~r~R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae~an 287 (408)
..+....+.+..|..+|..|+...|..|..+++.+...++..-
T Consensus 40 ~el~~A~~~L~~A~~a~~~~~y~~A~~~A~~A~~~A~~A~~~a 82 (103)
T PF14346_consen 40 VELKEAREKLQRAKAALDDGDYERARRLAEQAQADAELAEAKA 82 (103)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3667788889999999999999999999999999876665443
No 17
>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=65.25 E-value=8.4 Score=31.79 Aligned_cols=31 Identities=32% Similarity=0.279 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHcCChHHHHHHHHHHHHHHHH
Q 015358 252 QHSKAANNAYLRGDHFSAQQHSLKARKEWLI 282 (408)
Q Consensus 252 ~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ 282 (408)
-+..++..+|++||...|+++|.+|+.+...
T Consensus 39 ~~s~kv~~~~~~Gd~~~A~~aS~~Ak~~~~i 69 (82)
T PF04505_consen 39 VYSSKVRSRYAAGDYEGARRASRKAKKWSII 69 (82)
T ss_pred eechhhHHHHHCCCHHHHHHHHHHhHHHHHH
Confidence 3456789999999999999999999988743
No 18
>PF13763 DUF4167: Domain of unknown function (DUF4167)
Probab=56.20 E-value=49 Score=27.88 Aligned_cols=39 Identities=18% Similarity=0.152 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 015358 250 ASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNS 288 (408)
Q Consensus 250 R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae~an~ 288 (408)
-.+|.+-|..|-..||+-.|..|.+.|..|...+.++..
T Consensus 39 ~EKY~~LArDA~ssGDrV~aEny~QHAeHY~Ril~~~~~ 77 (80)
T PF13763_consen 39 IEKYNQLARDAQSSGDRVLAENYLQHAEHYFRILAAAQA 77 (80)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667799999999999999999999999887766654
No 19
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=50.44 E-value=61 Score=25.72 Aligned_cols=39 Identities=23% Similarity=0.119 Sum_probs=29.2
Q ss_pred HHHHHHHHH-HHHHHHHcCChHHHHHHHHHHHHHHHHHHH
Q 015358 247 MRSASQHSK-AANNAYLRGDHFSAQQHSLKARKEWLIAER 285 (408)
Q Consensus 247 ~r~R~~~~~-~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae~ 285 (408)
...|.+-|+ .|.+|=+.||-..|+.|-..++.+....+.
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 344555454 477888899999999999998888766544
No 20
>KOG4588 consensus Predicted ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=45.18 E-value=23 Score=35.31 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=31.9
Q ss_pred hccccchHHHHHHHHHhhccHHHHHHHHHhhhc
Q 015358 105 LHSWADNSLIEDLMEAVDNDIKRASNLLEGMVS 137 (408)
Q Consensus 105 ~~~wad~~li~dv~~a~~nd~~~a~~~L~~m~~ 137 (408)
|||..|-++|+-||.|--++|++|...|-+|..
T Consensus 1 Mfp~~Dye~ie~VlranlgavD~tid~llaM~~ 33 (267)
T KOG4588|consen 1 MFPYDDYEDIEGVLRANLGAVDRTIDDLLAMFP 33 (267)
T ss_pred CCCcchHHHHHHHHHHhcchHHHHHHHHHHhcc
Confidence 899999999999999999999999999999985
No 21
>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=44.23 E-value=31 Score=36.18 Aligned_cols=39 Identities=28% Similarity=0.243 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhccccchHHHHHHHHHhhccHHHHHHHHHhh
Q 015358 95 RDLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGM 135 (408)
Q Consensus 95 ~~~~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L~~m 135 (408)
+.-+|++||++ +.|.+++-.+|-|||.|-+.|..+|-..
T Consensus 337 E~~AIeRL~~L--GF~r~~viqaY~ACdKNEelAAn~Lf~~ 375 (378)
T TIGR00601 337 EKEAIERLCAL--GFDRGLVIQAYFACDKNEELAANYLLSQ 375 (378)
T ss_pred HHHHHHHHHHc--CCCHHHHHHHHHhcCCcHHHHHHHHHhh
Confidence 67899999999 7999999999999999999999999655
No 22
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=42.52 E-value=98 Score=27.57 Aligned_cols=41 Identities=29% Similarity=0.191 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHH
Q 015358 240 RKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEW 280 (408)
Q Consensus 240 RkeA~~~~r~R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~ 280 (408)
|..+....+...+.+..|...+..|+...|-.+|+||=+..
T Consensus 3 ~~~~~~~~~rA~~~l~~A~~~le~G~y~~a~f~aqQAvel~ 43 (132)
T COG2250 3 REEAEKWLRRAERDLKLAKRDLELGDYDLACFHAQQAVELA 43 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 66778888999999999999999999999999988765544
No 23
>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=41.01 E-value=1.6e+02 Score=25.99 Aligned_cols=55 Identities=15% Similarity=0.103 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015358 237 LVHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAA 291 (408)
Q Consensus 237 ~~~RkeA~~~~r~R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae~an~kAA 291 (408)
....+...++-....++..+|..+.+.|+...|+.|..+-+.+.+....+.....
T Consensus 11 ~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~~~ 65 (171)
T PF03357_consen 11 RRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQLS 65 (171)
T ss_dssp HHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566677777788889999999999999999999998888887777665443
No 24
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=40.06 E-value=33 Score=24.51 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=22.4
Q ss_pred cchHHHHHHHHHhhccHHHHHHHHHh
Q 015358 109 ADNSLIEDLMEAVDNDIKRASNLLEG 134 (408)
Q Consensus 109 ad~~li~dv~~a~~nd~~~a~~~L~~ 134 (408)
++..+|+.+|..+++++.+|...|.-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 57789999999999999999999864
No 25
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=34.82 E-value=2.1e+02 Score=28.05 Aligned_cols=51 Identities=24% Similarity=0.128 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 015358 234 DVYLVHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAE 284 (408)
Q Consensus 234 ~~Y~~~RkeA~~~~r~R~~~~~~Aa~Af~rGd~~aAk~lS~kAr~~~~~ae 284 (408)
+.+.+.|.++++..|.-.+++..|--+..+||...|...-.+|.+.-...+
T Consensus 13 ~e~d~~REE~l~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk 63 (204)
T COG2178 13 QEKDKAREEALKLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLK 63 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Confidence 568899999999999999999999999999998888776666665544443
No 26
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=21.69 E-value=2.3e+02 Score=20.26 Aligned_cols=34 Identities=21% Similarity=0.283 Sum_probs=25.7
Q ss_pred HHHHHHHhccccchHHHHHHHHHhhccHHHHHHHH
Q 015358 98 ALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (408)
Q Consensus 98 ~~~kL~~~~~wad~~li~dv~~a~~nd~~~a~~~L 132 (408)
++..+++.- .++.++-...|.++++|++.|+..-
T Consensus 3 ~i~~F~~iT-g~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 3 KIAQFMSIT-GADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHHH--SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHcCCCHHHHHHHH
Confidence 455666555 4688999999999999999998764
Done!