Query psy16216
Match_columns 129
No_of_seqs 101 out of 1041
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 23:48:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16216hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2095|consensus 99.9 6.8E-23 1.5E-27 174.6 6.8 119 1-128 96-227 (656)
2 PTZ00205 DNA polymerase kappa; 99.7 7E-19 1.5E-23 149.9 2.7 72 1-128 206-277 (571)
3 KOG2094|consensus 99.7 2E-17 4.3E-22 134.2 4.6 75 1-128 176-251 (490)
4 cd01703 PolY_Pol_iota DNA Poly 99.7 1.8E-17 3.9E-22 136.0 3.1 67 1-128 72-140 (379)
5 PRK01216 DNA polymerase IV; Va 99.7 2.2E-17 4.8E-22 134.2 2.5 69 1-128 81-149 (351)
6 cd00424 PolY Y-family of DNA p 99.7 2.5E-17 5.3E-22 132.8 2.4 69 1-128 75-144 (343)
7 cd01702 PolY_Pol_eta DNA Polym 99.6 9E-17 2E-21 131.0 4.2 60 1-128 94-153 (359)
8 cd01701 PolY_Rev1 DNA polymera 99.6 7.8E-17 1.7E-21 132.9 2.2 70 1-128 124-193 (404)
9 PRK03609 umuC DNA polymerase V 99.6 1.6E-16 3.5E-21 131.4 2.3 68 1-128 77-144 (422)
10 PRK03858 DNA polymerase IV; Va 99.6 2.4E-16 5.2E-21 129.0 2.4 69 1-128 76-144 (396)
11 COG0389 DinP Nucleotidyltransf 99.6 2.8E-16 6.1E-21 127.8 2.6 71 1-128 77-147 (354)
12 cd01700 PolY_Pol_V_umuC umuC s 99.6 4.2E-16 9.1E-21 125.6 3.4 68 1-128 75-142 (344)
13 PRK03103 DNA polymerase IV; Re 99.6 4.1E-16 8.8E-21 128.3 3.0 69 1-128 81-149 (409)
14 PRK02406 DNA polymerase IV; Va 99.6 3.2E-16 7E-21 126.2 1.8 69 1-128 71-139 (343)
15 cd03586 PolY_Pol_IV_kappa DNA 99.6 7E-16 1.5E-20 123.2 2.1 69 1-128 74-142 (334)
16 PRK03348 DNA polymerase IV; Pr 99.6 7.3E-16 1.6E-20 129.0 1.5 70 1-128 82-151 (454)
17 PRK01810 DNA polymerase IV; Va 99.6 1.1E-15 2.3E-20 125.8 2.0 68 1-128 83-150 (407)
18 PF00817 IMS: impB/mucB/samB f 99.5 3.2E-15 7E-20 107.6 3.8 69 1-128 73-142 (149)
19 PRK02794 DNA polymerase IV; Pr 99.5 3.1E-15 6.7E-20 123.7 4.0 70 1-128 111-180 (419)
20 PRK03352 DNA polymerase IV; Va 99.5 2E-15 4.2E-20 121.8 2.5 64 1-128 85-148 (346)
21 PRK14133 DNA polymerase IV; Pr 99.5 1.7E-15 3.8E-20 122.2 2.0 66 1-128 79-144 (347)
22 cd03468 PolY_like DNA Polymera 99.4 6.5E-14 1.4E-18 111.8 2.9 68 1-128 74-141 (335)
23 KOG2093|consensus 99.3 2.1E-12 4.6E-17 113.6 3.3 70 1-128 451-520 (1016)
24 COG2199 c-di-GMP synthetase (d 76.3 2.6 5.6E-05 30.1 2.6 28 100-127 115-149 (181)
25 PF14535 AMP-binding_C_2: AMP- 59.4 17 0.00038 23.8 3.7 24 100-123 53-76 (96)
26 TIGR02578 cas_TM1811_Csm1 CRIS 50.1 22 0.00047 31.7 3.8 28 100-127 597-627 (648)
27 cd07556 Nucleotidyl_cyc_III Cl 49.7 47 0.001 21.5 4.7 27 100-126 66-97 (133)
28 COG4071 Uncharacterized protei 45.9 44 0.00095 26.3 4.4 26 100-125 142-167 (278)
29 PF14824 Sirohm_synth_M: Siroh 42.7 30 0.00065 18.5 2.2 15 101-115 16-30 (30)
30 PF02873 MurB_C: UDP-N-acetyle 36.6 45 0.00097 22.7 2.9 19 101-119 79-97 (105)
31 KOG2095|consensus 34.7 27 0.00059 31.2 2.0 38 7-44 113-150 (656)
32 PRK09894 diguanylate cyclase; 34.3 32 0.00069 26.3 2.1 26 100-125 222-255 (296)
33 PF02541 Ppx-GppA: Ppx/GppA ph 30.6 83 0.0018 24.4 4.0 35 3-37 35-69 (285)
34 COG3706 PleD Response regulato 30.4 48 0.001 28.3 2.7 30 98-127 363-402 (435)
35 PF10678 DUF2492: Protein of u 28.4 45 0.00097 21.7 1.7 17 105-121 23-44 (78)
36 TIGR03853 matur_matur probable 27.7 49 0.0011 21.5 1.8 17 105-121 21-42 (77)
37 TIGR02577 cas_TM1794_Crm2 CRIS 27.4 69 0.0015 27.5 3.2 28 100-127 426-461 (482)
38 smart00267 GGDEF diguanylate c 27.2 60 0.0013 21.3 2.3 26 100-125 98-130 (163)
39 PRK00962 hypothetical protein; 26.0 49 0.0011 24.6 1.8 29 98-126 84-112 (165)
40 PF09016 Pas_Saposin: Pas fact 25.6 54 0.0012 21.1 1.7 14 105-118 21-34 (76)
41 COG4019 Uncharacterized protei 24.6 49 0.0011 23.9 1.5 32 5-36 49-81 (156)
42 PF06973 DUF1297: Domain of un 24.3 69 0.0015 24.3 2.3 18 96-113 163-180 (188)
43 COG0079 HisC Histidinol-phosph 23.1 25 0.00055 28.8 -0.2 26 7-33 166-191 (356)
44 PRK09438 nudB dihydroneopterin 23.1 74 0.0016 21.9 2.2 20 102-121 45-64 (148)
45 COG1353 Predicted CRISPR-assoc 23.0 79 0.0017 29.0 2.9 35 89-125 600-634 (799)
46 PLN02177 glycerol-3-phosphate 22.9 77 0.0017 27.4 2.7 21 100-120 452-472 (497)
47 PF02552 CO_dh: CO dehydrogena 21.2 58 0.0013 24.1 1.4 26 4-29 117-142 (167)
48 cd03675 Nudix_Hydrolase_2 Cont 20.6 89 0.0019 20.9 2.2 20 102-121 38-57 (134)
49 PF13592 HTH_33: Winged helix- 20.4 1.1E+02 0.0023 18.2 2.3 17 104-120 7-23 (60)
No 1
>KOG2095|consensus
Probab=99.88 E-value=6.8e-23 Score=174.62 Aligned_cols=119 Identities=34% Similarity=0.523 Sum_probs=94.2
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCc----cccccCCCcceeccCCC---------CCchHH
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGH----IAASQLSNTFVVGFGPD---------NNDEDA 67 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~----~~~~~l~~~~~~g~~~~---------~~~~~~ 67 (129)
||++|.+|+.+|..|.|+||++|+||+|+|+|+++.+++.++.- ..+...+..+..+.|.. ...+..
T Consensus 96 YR~as~ev~~~L~~y~~viek~~~dea~ld~tasvder~q~L~s~~~~~~~~~~p~~~~~~~~s~~~~~~~~~~~e~~~~ 175 (656)
T KOG2095|consen 96 YREASEEVKESLEPYRPVIEKASKDEAFLDLTASVDERLQDLQSDEFNMLLEEPPYGLIYGLPSALPNTREATNSENPLM 175 (656)
T ss_pred hhhhHHHHHHHHhhhHHHHHHHhhhhhhhhHHHHHHHHHHHHhhhhhhhhhhccchhcccCCccccchhhhhhhhccccc
Confidence 89999999999999999999999999999999999999988542 22455556666666541 022333
Q ss_pred hhhchhhhhccccCCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 68 RKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+.+....|+.. +-.+|+|+ +|.+|+.||.+||++|+.+||||||||||+|||
T Consensus 176 ~ee~~~~~~~~--------~d~~~~d~-~L~iGa~Iv~EiR~~i~~elg~tCSAGIa~NKm 227 (656)
T KOG2095|consen 176 REEIVSLWIEN--------DDFDWDDV-RLLIGAQIVKEIRDAIKLELGYTCSAGIAHNKM 227 (656)
T ss_pred hhhHhhhhhhc--------cccCchhh-hhHHHHHHHHHHHHHHHHHhCceeeccccccHH
Confidence 44455555532 11248998 899999999999999999999999999999997
No 2
>PTZ00205 DNA polymerase kappa; Provisional
Probab=99.74 E-value=7e-19 Score=149.88 Aligned_cols=72 Identities=19% Similarity=0.318 Sum_probs=62.6
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|+++|.+|+|.+|.+||||+|||||++.....
T Consensus 206 Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~~~----------------------------------------- 244 (571)
T PTZ00205 206 YNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIERFE----------------------------------------- 244 (571)
T ss_pred HHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhhcc-----------------------------------------
Confidence 899999999999999999999999999999999764200
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+. ..+.++|++||++|+++||||||||||+||+
T Consensus 245 --~~-------------~~~~~iA~~IR~~I~~~tgLt~SiGIA~Nkl 277 (571)
T PTZ00205 245 --GT-------------KTAEDVASELRVRVFGETKLTASAGIGPTAA 277 (571)
T ss_pred --CC-------------CCHHHHHHHHHHHHHHHHCCcEEEEEcCCHH
Confidence 00 0146899999999999999999999999996
No 3
>KOG2094|consensus
Probab=99.69 E-value=2e-17 Score=134.21 Aligned_cols=75 Identities=37% Similarity=0.492 Sum_probs=64.1
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+.+|++|.+||.+|+|.+-..|+||||||+|..++.+-
T Consensus 176 Yt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~~----------------------------------------- 214 (490)
T KOG2094|consen 176 YTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRERE----------------------------------------- 214 (490)
T ss_pred HHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHhh-----------------------------------------
Confidence 899999999999999999999999999999999987541
Q ss_pred CCCCccccCChHHHHHHHH-HHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAI-AGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~-aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+|.. ... +.+++++||.+|+++||+|||||||+|+|
T Consensus 215 -~g~l-----------~~nG~~evveeiR~rV~qeTglT~SaGIAaN~l 251 (490)
T KOG2094|consen 215 -LGFL-----------VENGITEVVEEIRFRVEQETGLTCSAGIAANKL 251 (490)
T ss_pred -cchh-----------hhccHHHHHHHHHHHHHHhcCceeeccccHhHH
Confidence 0100 000 46899999999999999999999999987
No 4
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=99.67 E-value=1.8e-17 Score=136.04 Aligned_cols=67 Identities=33% Similarity=0.565 Sum_probs=61.0
Q ss_pred ChHHHHHHHHHHHhcch--hhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcc
Q psy16216 1 YRNAGREVIAVLSEFSN--IVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQ 78 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p--~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 78 (129)
|+++|++|++++++|+| .||.+||||+|||+|+...
T Consensus 72 Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~------------------------------------------ 109 (379)
T cd01703 72 FRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRL------------------------------------------ 109 (379)
T ss_pred HHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccc------------------------------------------
Confidence 89999999999999999 9999999999999997631
Q ss_pred ccCCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 79 VYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
..+.++|++||++|+++||||||||||+||+
T Consensus 110 -------------------~~g~~la~~ir~~I~~~~Glt~siGIa~nk~ 140 (379)
T cd01703 110 -------------------LVASHIAYEMRERIENELGLTCCAGIASNKL 140 (379)
T ss_pred -------------------hhHHHHHHHHHHHHHHHhCCeEEEEEcCCHH
Confidence 1247899999999999999999999999995
No 5
>PRK01216 DNA polymerase IV; Validated
Probab=99.66 E-value=2.2e-17 Score=134.24 Aligned_cols=69 Identities=38% Similarity=0.600 Sum_probs=62.2
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+|+||+|||||+..+.
T Consensus 81 y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~~l------------------------------------------- 117 (351)
T PRK01216 81 YQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKVKN------------------------------------------- 117 (351)
T ss_pred HHHHHHHHHHHHHHhCCceEEccCCeEEEEcccchhc-------------------------------------------
Confidence 8999999999999999999999999999999998651
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++. +..++++||++|++++|||||+|||+||+
T Consensus 118 -~g~---------------~~~la~~ir~~I~~~~glt~siGia~nk~ 149 (351)
T PRK01216 118 -YQD---------------AYNLGLEIKNKILEKEKITVTVGISKNKV 149 (351)
T ss_pred -cCC---------------HHHHHHHHHHHHHHHHCCcEEEEecCCHH
Confidence 111 46899999999999999999999999986
No 6
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=99.66 E-value=2.5e-17 Score=132.78 Aligned_cols=69 Identities=30% Similarity=0.448 Sum_probs=61.8
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||||+..+.
T Consensus 75 y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~~------------------------------------------- 111 (343)
T cd00424 75 YRRLSERLLSELEEVAPLVEVASIDELFLDLTGSARL------------------------------------------- 111 (343)
T ss_pred HHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchhc-------------------------------------------
Confidence 8899999999999999999999999999999997641
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhC-ceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQ-FHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lg-ltcSaGIa~NKl 128 (129)
++ .+.++|++||++|++++| ||||+|||+||+
T Consensus 112 -~~---------------~~~~la~~i~~~i~~~~ggl~~siGia~n~~ 144 (343)
T cd00424 112 -LG---------------LGSEVALRIKRHIAEQLGGITASIGIASNKL 144 (343)
T ss_pred -cC---------------CHHHHHHHHHHHHHHHhCCceEEEeecccHH
Confidence 01 146899999999999998 999999999986
No 7
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=99.65 E-value=9e-17 Score=131.01 Aligned_cols=60 Identities=55% Similarity=0.928 Sum_probs=56.3
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||+.
T Consensus 94 Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv~------------------------------------------------ 125 (359)
T cd01702 94 YRRASRKILNILKRFGDVVEKASIDEAYLDLG------------------------------------------------ 125 (359)
T ss_pred HHHHHHHHHHHHHHcCCceEECcCCeeHHHHH------------------------------------------------
Confidence 89999999999999999999999999999981
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
.++|.+||++|++++|||||||||+||+
T Consensus 126 --------------------~~la~~ir~~I~~~~glt~SiGIa~nk~ 153 (359)
T cd01702 126 --------------------SRIVEEIRQQVYDELGYTCSAGIAHNKM 153 (359)
T ss_pred --------------------HHHHHHHHHHHHHHhCccEEeeecCCHH
Confidence 2588999999999999999999999996
No 8
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=99.63 E-value=7.8e-17 Score=132.88 Aligned_cols=70 Identities=27% Similarity=0.434 Sum_probs=61.9
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||||+..+. +
T Consensus 124 Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~-~----------------------------------------- 161 (404)
T cd01701 124 YEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEE-T----------------------------------------- 161 (404)
T ss_pred HHHHHHHHHHHHHHhCCceEEcccceEEEEccccccc-c-----------------------------------------
Confidence 7899999999999999999999999999999997531 0
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++ .+..++++||++|++++|||||+|||+||+
T Consensus 162 -~~---------------~~~~la~~ir~~I~~~~gl~~siGia~nk~ 193 (404)
T cd01701 162 -YE---------------LPEELAEAIRNEIRETTGCSASVGIGPNIL 193 (404)
T ss_pred -cC---------------CHHHHHHHHHHHHHHHHCCCEEEEEcCCHH
Confidence 01 146899999999999999999999999996
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=99.61 E-value=1.6e-16 Score=131.43 Aligned_cols=68 Identities=40% Similarity=0.492 Sum_probs=60.8
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||||+..+ +
T Consensus 77 y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~--l----------------------------------------- 113 (422)
T PRK03609 77 YADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRN--C----------------------------------------- 113 (422)
T ss_pred HHHHHHHHHHHHHHhCCCceEeccccceecCCCCcC--C-----------------------------------------
Confidence 889999999999999999999999999999998743 1
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+ -...++++||++|++++|||||||||+||+
T Consensus 114 --~---------------~~~~~a~~i~~~I~~~~gl~~siGia~n~~ 144 (422)
T PRK03609 114 --R---------------DLTDFGREIRATVLQRTHLTVGVGIAQTKT 144 (422)
T ss_pred --C---------------CHHHHHHHHHHHHHHHHCCceEEEecCCHH
Confidence 0 035789999999999999999999999986
No 10
>PRK03858 DNA polymerase IV; Validated
Probab=99.60 E-value=2.4e-16 Score=129.01 Aligned_cols=69 Identities=26% Similarity=0.436 Sum_probs=61.7
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||||+..+ +
T Consensus 76 y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~~--~----------------------------------------- 112 (396)
T PRK03858 76 YSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLRR--I----------------------------------------- 112 (396)
T ss_pred HHHHHHHHHHHHHHhCCceEEecCCeEEEEcccccc--c-----------------------------------------
Confidence 789999999999999999999999999999999754 1
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+++ +..++++||++|++++|||||+|||+||+
T Consensus 113 -~~~---------------~~~la~~ir~~i~~~~gl~~svGia~n~~ 144 (396)
T PRK03858 113 -SGT---------------PVQIAARLRRRVREEVGLPITVGVARTKF 144 (396)
T ss_pred -cCC---------------HHHHHHHHHHHHHHHHCCCeEEEEcCChH
Confidence 111 36799999999999999999999999986
No 11
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=99.60 E-value=2.8e-16 Score=127.78 Aligned_cols=71 Identities=42% Similarity=0.543 Sum_probs=62.3
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+.+|.+|++|+++|+|.||.+||||+|||+|+....
T Consensus 77 y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~~------------------------------------------- 113 (354)
T COG0389 77 YRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALRL------------------------------------------- 113 (354)
T ss_pred HHHHHHHHHHHHHhccccceeeeccceeeeccccccc-------------------------------------------
Confidence 8899999999999999999999999999999876531
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
.+ +..+.++|.+||+.|++++|||||+|||+||+
T Consensus 114 -~g-------------~~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~ 147 (354)
T COG0389 114 -LG-------------LADAPRIALEIRFGILLELGLTASVGISDNKF 147 (354)
T ss_pred -CC-------------cccHHHHHHHHHHHHHHhhCCEEEEEecCcHH
Confidence 01 11368999999999999999999999999996
No 12
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=99.60 E-value=4.2e-16 Score=125.58 Aligned_cols=68 Identities=32% Similarity=0.541 Sum_probs=61.2
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+|+||+|||+|+..+ +
T Consensus 75 y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~--~----------------------------------------- 111 (344)
T cd01700 75 YGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR--F----------------------------------------- 111 (344)
T ss_pred HHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC--C-----------------------------------------
Confidence 789999999999999999999999999999998653 1
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++ +..+|++||++|++++|||||+|||+||+
T Consensus 112 --~~---------------~~~la~~i~~~i~~~~gl~~s~Gia~~~~ 142 (344)
T cd01700 112 --GD---------------LEELARKIRRRILQETGIPVTVGIGPTKT 142 (344)
T ss_pred --CC---------------HHHHHHHHHHHHHHHhCCceEEEecCCHH
Confidence 11 36899999999999999999999999986
No 13
>PRK03103 DNA polymerase IV; Reviewed
Probab=99.59 E-value=4.1e-16 Score=128.32 Aligned_cols=69 Identities=26% Similarity=0.433 Sum_probs=61.8
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+|+||+|||||+..+.
T Consensus 81 y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~~~------------------------------------------- 117 (409)
T PRK03103 81 YIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQKL------------------------------------------- 117 (409)
T ss_pred HHHHHHHHHHHHHHhCccceecCCCeeEeeccchhhc-------------------------------------------
Confidence 7899999999999999999999999999999998641
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+++ ...++++||++|++++|||||+|||+||+
T Consensus 118 -~~~---------------~~~la~~ir~~i~~~~gl~~svGia~n~~ 149 (409)
T PRK03103 118 -FGS---------------PLEIAQKIQQRIMRETGVYARVGIGPNKL 149 (409)
T ss_pred -CCC---------------HHHHHHHHHHHHHHHHCceEEEeecCCHH
Confidence 111 35799999999999999999999999985
No 14
>PRK02406 DNA polymerase IV; Validated
Probab=99.59 E-value=3.2e-16 Score=126.21 Aligned_cols=69 Identities=32% Similarity=0.566 Sum_probs=61.8
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|+.++.+|+|.||.+|+||+|||+|+..+.
T Consensus 71 y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~~------------------------------------------- 107 (343)
T PRK02406 71 YKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNKLC------------------------------------------- 107 (343)
T ss_pred HHHHHHHHHHHHHHhCCceEEccCCeEEEeccCcccc-------------------------------------------
Confidence 7899999999999999999999999999999997641
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++. +..+++.||++|++++|||||+|||+||+
T Consensus 108 -~~~---------------~~~la~~i~~~i~~~~gl~~siGia~n~~ 139 (343)
T PRK02406 108 -IGS---------------ATLIAQEIRQDIFEELGLTASAGVAPNKF 139 (343)
T ss_pred -CCC---------------HHHHHHHHHHHHHHHHCCCeEEEeccCHH
Confidence 111 36899999999999999999999999986
No 15
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=99.57 E-value=7e-16 Score=123.16 Aligned_cols=69 Identities=45% Similarity=0.639 Sum_probs=61.8
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+|+||+|+|+|++...
T Consensus 74 y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~~~------------------------------------------- 110 (334)
T cd03586 74 YREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRL------------------------------------------- 110 (334)
T ss_pred HHHHHHHHHHHHHHcCCceEEecccceeEcccccccc-------------------------------------------
Confidence 7899999999999999999999999999999987541
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++ .+..++.+||++|++++|||||+|||+||+
T Consensus 111 -~~---------------~~~~la~~ir~~i~~~~g~~~siGia~n~~ 142 (334)
T cd03586 111 -FG---------------SATEIAKEIRARIREETGLTASAGIAPNKF 142 (334)
T ss_pred -CC---------------CHHHHHHHHHHHHHHHHCCceEEEEhhcHH
Confidence 11 146899999999999999999999999985
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=99.56 E-value=7.3e-16 Score=128.99 Aligned_cols=70 Identities=31% Similarity=0.477 Sum_probs=60.4
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||++.....
T Consensus 82 Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~~~------------------------------------------- 118 (454)
T PRK03348 82 YRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELAGA------------------------------------------- 118 (454)
T ss_pred HHHHHHHHHHHHHHhCCceEEecCCeEEEEccccccc-------------------------------------------
Confidence 8999999999999999999999999999997765421
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
... .+..++++||++|++++|||||+|||+||+
T Consensus 119 ---~~~------------~~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~ 151 (454)
T PRK03348 119 ---SAE------------EVEAFAERLRARVREETGLPASVGAGSGKQ 151 (454)
T ss_pred ---cCC------------CHHHHHHHHHHHHHHHHCCCeEEEEcCCHH
Confidence 000 146799999999999999999999999986
No 17
>PRK01810 DNA polymerase IV; Validated
Probab=99.55 E-value=1.1e-15 Score=125.78 Aligned_cols=68 Identities=41% Similarity=0.671 Sum_probs=60.9
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+|+||+|||||++.. +
T Consensus 83 y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~--~----------------------------------------- 119 (407)
T PRK01810 83 YREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYA--L----------------------------------------- 119 (407)
T ss_pred HHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccc--c-----------------------------------------
Confidence 889999999999999999999999999999998653 1
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+ -+.++++.||++|++++|+|||+|||+||+
T Consensus 120 -~----------------~~~~~a~~i~~~i~~~~gl~~svGia~n~~ 150 (407)
T PRK01810 120 -G----------------SPLEIAKMIQQRLLTELQLPCSIGIAPNKF 150 (407)
T ss_pred -C----------------CHHHHHHHHHHHHHHHHCCceEEEEcCCHH
Confidence 0 035789999999999999999999999986
No 18
>PF00817 IMS: impB/mucB/samB family; InterPro: IPR001126 In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA. This machinery allows the replication to continue through DNA lesion, and therefore avoid lethal interruption of DNA replication after DNA damage []. UmuC is a well conserved protein in prokaryotes, with a homologue in yeast species. Proteins currently known to belong to this family are listed below: E. coli MucB protein. Plasmid-born analogue of the UmuC protein. Saccharomyces cerevisiae (Baker's yeast) Rev1 protein. Homologue of UmuC also required for normal induction of mutations by physical and chemical agents. Salmonella typhimurium ImpB protein. Plasmid-born analogue of the UmuC protein. Bacterial UmuC protein. E. coli DNA-damage-inducible protein P (DinP). S. typhimurium SamB homologue of UmuC plasmid associated. ; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3BJY_A 2AQ4_A 3OSP_A 4DL7_A 4DL6_A 3TQ1_A 3MR2_A 4EEY_A 3MR3_A 4DL4_A ....
Probab=99.55 E-value=3.2e-15 Score=107.65 Aligned_cols=69 Identities=30% Similarity=0.439 Sum_probs=59.2
Q ss_pred ChHHHHHHHHHHHhc-chhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhccc
Q psy16216 1 YRNAGREVIAVLSEF-SNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQV 79 (129)
Q Consensus 1 Yr~~S~~I~~il~~~-~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~ 79 (129)
|+++|++|+.++.+| .|.||.+|+||+|+|+|+..+.
T Consensus 73 ~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~l------------------------------------------ 110 (149)
T PF00817_consen 73 YREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLRL------------------------------------------ 110 (149)
T ss_dssp HHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHHH------------------------------------------
T ss_pred HHHHHHHHHHHHHhcccccceecccccccccCCcchhh------------------------------------------
Confidence 789999999999999 7799999999999999997652
Q ss_pred cCCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 80 YSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 80 ~~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+.....++++||++|++++||+||+|||+||+
T Consensus 111 -----------------~~~~~~~~~~l~~~i~~~~gl~~s~Gia~~~~ 142 (149)
T PF00817_consen 111 -----------------FGGEEALARRLRQAIAEETGLTASIGIAPNPL 142 (149)
T ss_dssp -----------------HHHHHHHHHHHHHHHHHHHS--EEEEEESSHH
T ss_pred -----------------cchHHHHHHHHHHHHHHHhCCEEEEEEeCCHH
Confidence 11236899999999999999999999999985
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=99.54 E-value=3.1e-15 Score=123.68 Aligned_cols=70 Identities=30% Similarity=0.488 Sum_probs=60.5
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+|+||+|||+|+..+ +
T Consensus 111 y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~--l----------------------------------------- 147 (419)
T PRK02794 111 YVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTER--L----------------------------------------- 147 (419)
T ss_pred HHHHHHHHHHHHHHhCcceeeccCCeEEEeccchhh--h-----------------------------------------
Confidence 889999999999999999999999999999998764 1
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++.. .+.++.+||++|++++|||||+|||+||+
T Consensus 148 -~g~~--------------~~~~~~~i~~~i~~~~gl~~svGIa~n~~ 180 (419)
T PRK02794 148 -HGAP--------------PAVVLARFARRVEREIGITVSVGLSYNKF 180 (419)
T ss_pred -cCCC--------------HHHHHHHHHHHHHHHHCCceEEEEcCCHH
Confidence 1110 24567899999999999999999999985
No 20
>PRK03352 DNA polymerase IV; Validated
Probab=99.54 E-value=2e-15 Score=121.78 Aligned_cols=64 Identities=41% Similarity=0.601 Sum_probs=59.0
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|+.++.+|+|.||.+|+||+|||+|+. .
T Consensus 85 y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~-~-------------------------------------------- 119 (346)
T PRK03352 85 YDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTD-D-------------------------------------------- 119 (346)
T ss_pred HHHHHHHHHHHHHHhCCceEEecCccEEEeCCCC-C--------------------------------------------
Confidence 8899999999999999999999999999999863 0
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
...+++.||++|++++|||||+|||+||+
T Consensus 120 -------------------~~~la~~ir~~i~~~~gl~~siGia~nk~ 148 (346)
T PRK03352 120 -------------------PEALAEEIRAAVLERTGLSCSVGIGDNKL 148 (346)
T ss_pred -------------------HHHHHHHHHHHHHHHHCCCEEEeecCCHH
Confidence 25799999999999999999999999985
No 21
>PRK14133 DNA polymerase IV; Provisional
Probab=99.54 E-value=1.7e-15 Score=122.23 Aligned_cols=66 Identities=35% Similarity=0.551 Sum_probs=60.0
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|+++|++|++++.+|+|.||.+||||+|||+|+...
T Consensus 79 y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~~-------------------------------------------- 114 (347)
T PRK14133 79 YKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIKE-------------------------------------------- 114 (347)
T ss_pred HHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCCC--------------------------------------------
Confidence 789999999999999999999999999999997421
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
+ ...++++||++|++++|||||+|||+||+
T Consensus 115 ---~---------------~~~la~~i~~~i~~~~gl~~siGia~n~~ 144 (347)
T PRK14133 115 ---E---------------PIKIAKYIKKKVKKETGLTLSVGISYNKF 144 (347)
T ss_pred ---C---------------HHHHHHHHHHHHHHHHCCcEEEEEcCcHH
Confidence 0 35799999999999999999999999986
No 22
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=99.42 E-value=6.5e-14 Score=111.75 Aligned_cols=68 Identities=24% Similarity=0.253 Sum_probs=58.9
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|.++|++|++++.+|+|.||.+|+||+|||+|+..+.
T Consensus 74 y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~~~------------------------------------------- 110 (335)
T cd03468 74 DARALQELALWLLRFTPLVALDGPDGLLLDVTGCLHL------------------------------------------- 110 (335)
T ss_pred HHHHHHHHHHHHHhcCCccccCCCCeEEEEcccchhh-------------------------------------------
Confidence 7899999999999999999999999999999997541
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
++. ...++..||+.+. ++|++||+|||+||+
T Consensus 111 -~~~---------------~~~~a~~i~~~~~-~~gl~~siGia~n~~ 141 (335)
T cd03468 111 -FGG---------------EDALAASLRAALA-TLGLSARAGIADTPG 141 (335)
T ss_pred -cCC---------------HHHHHHHHHHHHH-HcCCeEEEEecCCHH
Confidence 111 3568899999985 689999999999985
No 23
>KOG2093|consensus
Probab=99.27 E-value=2.1e-12 Score=113.57 Aligned_cols=70 Identities=30% Similarity=0.514 Sum_probs=62.0
Q ss_pred ChHHHHHHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCccccccCCCcceeccCCCCCchHHhhhchhhhhcccc
Q psy16216 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVY 80 (129)
Q Consensus 1 Yr~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
|.++|+.++++|++|.-.||.+|+||+|+|+|......
T Consensus 451 Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~------------------------------------------ 488 (1016)
T KOG2093|consen 451 YKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEE------------------------------------------ 488 (1016)
T ss_pred HHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhh------------------------------------------
Confidence 78999999999999999999999999999999987531
Q ss_pred CCCCccccCChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccCCCC
Q psy16216 81 SDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128 (129)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~NKl 128 (129)
. . ..+.+|..||+.|++.||++||||||.|+|
T Consensus 489 ---~------------~-tp~~la~~IRqEI~e~TgC~aS~Gig~t~L 520 (1016)
T KOG2093|consen 489 ---N------------E-TPAVLAEHIRQEILEKTGCPASAGIGGTML 520 (1016)
T ss_pred ---c------------c-CHHHHHHHHHHHHHhccCCceeeccchHHH
Confidence 0 0 137899999999999999999999999875
No 24
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=76.27 E-value=2.6 Score=30.13 Aligned_cols=28 Identities=32% Similarity=0.342 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHhh-------CceeeecccCCC
Q psy16216 100 AGVIVEEIRAAVLSKT-------QFHCSAGIAHNK 127 (129)
Q Consensus 100 aa~ia~~iR~~I~~~l-------gltcSaGIa~NK 127 (129)
+..++.+||+.|.... .+|||+||+...
T Consensus 115 ~~~~~~~l~~~~~~~~~~~~~~~~~t~siGi~~~~ 149 (181)
T COG2199 115 AARLAERIRAALEEPFFLGGEELRVTVSIGVALYP 149 (181)
T ss_pred HHHHHHHHHHHHHcccccCCceEEEEEEEEEEecC
Confidence 5677777777776654 489999998653
No 25
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=59.44 E-value=17 Score=23.77 Aligned_cols=24 Identities=8% Similarity=0.113 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHhhCceeeecc
Q psy16216 100 AGVIVEEIRAAVLSKTQFHCSAGI 123 (129)
Q Consensus 100 aa~ia~~iR~~I~~~lgltcSaGI 123 (129)
..+++.+|+++|++.+|++|.+=+
T Consensus 53 ~~~l~~~i~~~lk~~lgv~~~V~l 76 (96)
T PF14535_consen 53 LEALAERIAERLKERLGVRPEVEL 76 (96)
T ss_dssp HHHHHHHHHHHHHHHHSS-EEEEE
T ss_pred HHHHHHHHHHHHHhhcCceEEEEE
Confidence 478999999999999999998744
No 26
>TIGR02578 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. A typical example is TM1811 from Thermotoga maritima. CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This protein family belongs to a conserved gene cluster regularly found near CRISPR repeats.
Probab=50.13 E-value=22 Score=31.73 Aligned_cols=28 Identities=21% Similarity=0.124 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHhhC---ceeeecccCCC
Q psy16216 100 AGVIVEEIRAAVLSKTQ---FHCSAGIAHNK 127 (129)
Q Consensus 100 aa~ia~~iR~~I~~~lg---ltcSaGIa~NK 127 (129)
+-++|.+||+...+.++ +|.|+||+.-+
T Consensus 597 ~l~~A~~i~~~F~~~~~~~~~TlSaGi~i~~ 627 (648)
T TIGR02578 597 VLELASDIREYFEKFTCRDKITISAGVVVVS 627 (648)
T ss_pred HHHHHHHHHHHHHHHhCCCCeeEEEEEEECC
Confidence 36788888888887774 99999997654
No 27
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=49.73 E-value=47 Score=21.49 Aligned_cols=27 Identities=26% Similarity=0.327 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHhh-----CceeeecccCC
Q psy16216 100 AGVIVEEIRAAVLSKT-----QFHCSAGIAHN 126 (129)
Q Consensus 100 aa~ia~~iR~~I~~~l-----gltcSaGIa~N 126 (129)
+.+++.+|++.+.+.. ++++++|++..
T Consensus 66 ~~~~~~~i~~~~~~~~~~~~~~~~~~ig~~~g 97 (133)
T cd07556 66 AVAFAEDMREAVSALNQSEGNPVRVRIGIHTG 97 (133)
T ss_pred HHHHHHHHHHHHHHHHhccCCceEEEEEEecc
Confidence 4566777777764432 57778777643
No 28
>COG4071 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.90 E-value=44 Score=26.27 Aligned_cols=26 Identities=12% Similarity=0.152 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHhhCceeeecccC
Q psy16216 100 AGVIVEEIRAAVLSKTQFHCSAGIAH 125 (129)
Q Consensus 100 aa~ia~~iR~~I~~~lgltcSaGIa~ 125 (129)
+..+|++|++.|++++|..+++=|+.
T Consensus 142 p~~vA~el~~Ei~rr~GvDV~v~v~D 167 (278)
T COG4071 142 PKKVAEELYKEIKRRLGVDVVVMVAD 167 (278)
T ss_pred hHHHHHHHHHHHHHHhCCceEEEEec
Confidence 46899999999999999998886654
No 29
>PF14824 Sirohm_synth_M: Sirohaem biosynthesis protein central; PDB: 1KYQ_B.
Probab=42.74 E-value=30 Score=18.48 Aligned_cols=15 Identities=13% Similarity=0.045 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHhh
Q psy16216 101 GVIVEEIRAAVLSKT 115 (129)
Q Consensus 101 a~ia~~iR~~I~~~l 115 (129)
=.+|+.||++|.+.+
T Consensus 16 P~la~~iR~~ie~~l 30 (30)
T PF14824_consen 16 PRLARLIRKEIERLL 30 (30)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhC
Confidence 368999999998754
No 30
>PF02873 MurB_C: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; InterPro: IPR011601 This entry represents a C-terminal conserved region of UDP-N-acetylenolpyruvoylglucosamine reductase 1.1.1.158 from EC, which is also called UDP-N-acetylmuramate dehydrogenase. It is a part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide, which is a precursor of bacterial peptidoglycan. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 1MBB_A 2Q85_A 2MBR_A 1UXY_A 1MBT_A 1HSK_A 2GQU_A 2GQT_A 3I99_A 3TX1_A.
Probab=36.63 E-value=45 Score=22.70 Aligned_cols=19 Identities=26% Similarity=0.307 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHhhCcee
Q psy16216 101 GVIVEEIRAAVLSKTQFHC 119 (129)
Q Consensus 101 a~ia~~iR~~I~~~lgltc 119 (129)
..++..||++|++++|++-
T Consensus 79 ~~Li~~v~~~V~~~~Gi~L 97 (105)
T PF02873_consen 79 LALIEEVRERVKEKFGIEL 97 (105)
T ss_dssp HHHHHHHHHHHHHHHS--B
T ss_pred HHHHHHHHHHHHHHHCCee
Confidence 6899999999999999753
No 31
>KOG2095|consensus
Probab=34.72 E-value=27 Score=31.24 Aligned_cols=38 Identities=16% Similarity=0.024 Sum_probs=29.1
Q ss_pred HHHHHHHhcchhhhhcccchhhhhccHHHHHHHHhcCc
Q psy16216 7 EVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGH 44 (129)
Q Consensus 7 ~I~~il~~~~p~ve~~SiDEaylDlT~~v~~~l~~~~~ 44 (129)
.|-.+...-+..++.++|||.|+||+.-+...+.+..|
T Consensus 113 viek~~~dea~ld~tasvder~q~L~s~~~~~~~~~~p 150 (656)
T KOG2095|consen 113 VIEKASKDEAFLDLTASVDERLQDLQSDEFNMLLEEPP 150 (656)
T ss_pred HHHHHhhhhhhhhHHHHHHHHHHHHhhhhhhhhhhccc
Confidence 56666666677999999999999999777655555444
No 32
>PRK09894 diguanylate cyclase; Provisional
Probab=34.32 E-value=32 Score=26.27 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHh--------hCceeeecccC
Q psy16216 100 AGVIVEEIRAAVLSK--------TQFHCSAGIAH 125 (129)
Q Consensus 100 aa~ia~~iR~~I~~~--------lgltcSaGIa~ 125 (129)
+..++.+|+..|.+. +.+++|+||+.
T Consensus 222 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~siGv~~ 255 (296)
T PRK09894 222 ACRAGERIRQLIANHAITHSDGRINITATFGVSR 255 (296)
T ss_pred HHHHHHHHHHHHHhCCcccCCceEEEEEEEEEEE
Confidence 567888888888643 46889999875
No 33
>PF02541 Ppx-GppA: Ppx/GppA phosphatase family; InterPro: IPR003695 Exopolyphosphate phosphatase (Ppx) 3.6.1.11 from EC and guanosine pentaphosphate phosphatase (GppA) 3.6.1.40 from EC belong to the sugar kinase/actin/hsp70 superfamily [].; PDB: 3MDQ_A 1U6Z_A 1T6D_B 2J4R_B 1T6C_A 2FLO_B 3CER_B 3HI0_A.
Probab=30.61 E-value=83 Score=24.41 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhcchhhhhcccchhhhhccHHHHH
Q psy16216 3 NAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37 (129)
Q Consensus 3 ~~S~~I~~il~~~~p~ve~~SiDEaylDlT~~v~~ 37 (129)
+.-.++.++|++|....+.++++..++=-|..+++
T Consensus 35 e~i~r~~~~L~~f~~~~~~~~v~~i~~vATsA~R~ 69 (285)
T PF02541_consen 35 EAIERAIDALKRFKEILKDYGVEKIRAVATSALRE 69 (285)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTGSEEEEEEEHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEhhHHHHh
Confidence 34467888999999999999998888877888763
No 34
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=30.41 E-value=48 Score=28.29 Aligned_cols=30 Identities=30% Similarity=0.331 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHH----------hhCceeeecccCCC
Q psy16216 98 AIAGVIVEEIRAAVLS----------KTQFHCSAGIAHNK 127 (129)
Q Consensus 98 ~~aa~ia~~iR~~I~~----------~lgltcSaGIa~NK 127 (129)
..|..++.+||..|.. .+.+|.|+|||.-+
T Consensus 363 ~~Ai~iaerIr~~i~~~~~~~~~~~~~~~~TiSiGVa~~~ 402 (435)
T COG3706 363 EAAIAIAERIRQKINELPFVHELSREPLEVTISIGVAEGK 402 (435)
T ss_pred HHHHHHHHHHHHHHhcCCccccccccceEEEEEEEEEecC
Confidence 3578899999999872 25589999998754
No 35
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=28.38 E-value=45 Score=21.74 Aligned_cols=17 Identities=47% Similarity=0.770 Sum_probs=13.4
Q ss_pred HHHHHHHHHhhC-----ceeee
Q psy16216 105 EEIRAAVLSKTQ-----FHCSA 121 (129)
Q Consensus 105 ~~iR~~I~~~lg-----ltcSa 121 (129)
.+|+++|.+++| +|||+
T Consensus 23 ~~L~~ai~~~FG~~arFhTCSa 44 (78)
T PF10678_consen 23 EELKAAIIEKFGEDARFHTCSA 44 (78)
T ss_pred HHHHHHHHHHhCCCceEEecCC
Confidence 457778888888 88986
No 36
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=27.66 E-value=49 Score=21.55 Aligned_cols=17 Identities=41% Similarity=0.595 Sum_probs=13.4
Q ss_pred HHHHHHHHHhhC-----ceeee
Q psy16216 105 EEIRAAVLSKTQ-----FHCSA 121 (129)
Q Consensus 105 ~~iR~~I~~~lg-----ltcSa 121 (129)
..++..|.+++| .|||+
T Consensus 21 ~~L~~~i~~~FG~~arFhTCSa 42 (77)
T TIGR03853 21 ESLKAAIEQKFGEDARFHTCSA 42 (77)
T ss_pred HHHHHHHHHHhCCCceEeeccc
Confidence 456788888888 78886
No 37
>TIGR02577 cas_TM1794_Crm2 CRISPR-associated protein, Crm2 family. This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This protein, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2.
Probab=27.41 E-value=69 Score=27.49 Aligned_cols=28 Identities=21% Similarity=0.122 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHhh--------CceeeecccCCC
Q psy16216 100 AGVIVEEIRAAVLSKT--------QFHCSAGIAHNK 127 (129)
Q Consensus 100 aa~ia~~iR~~I~~~l--------gltcSaGIa~NK 127 (129)
+-++|..||+...+.+ .+|.|+||+..+
T Consensus 426 al~~a~~l~~~F~~~~~~~~~~~~~~T~SaGI~iah 461 (482)
T TIGR02577 426 ALDVAKELRKEFRESLEKSLGGERGPTMSAGLLIVH 461 (482)
T ss_pred HHHHHHHHHHHHHHHhhcccccCCCceEEEEEEEeC
Confidence 4566666666655544 489999987544
No 38
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=27.16 E-value=60 Score=21.34 Aligned_cols=26 Identities=23% Similarity=0.211 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHhhC-------ceeeecccC
Q psy16216 100 AGVIVEEIRAAVLSKTQ-------FHCSAGIAH 125 (129)
Q Consensus 100 aa~ia~~iR~~I~~~lg-------ltcSaGIa~ 125 (129)
+..++.+|+..+.+... +++++|++.
T Consensus 98 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~ 130 (163)
T smart00267 98 AIALAERILQQLREPIIIHGIPLYLTISIGVAA 130 (163)
T ss_pred HHHHHHHHHHHHhCccccCCcEEEEEEEEEEEe
Confidence 35667777777776655 899999976
No 39
>PRK00962 hypothetical protein; Provisional
Probab=26.01 E-value=49 Score=24.62 Aligned_cols=29 Identities=17% Similarity=0.322 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHhhCceeeecccCC
Q psy16216 98 AIAGVIVEEIRAAVLSKTQFHCSAGIAHN 126 (129)
Q Consensus 98 ~~aa~ia~~iR~~I~~~lgltcSaGIa~N 126 (129)
.+|..+|+-+|+..--..++-.||||+..
T Consensus 84 ~vA~~MA~~vr~~l~aDiaI~tTAGiGrG 112 (165)
T PRK00962 84 LVAKLMAEALKNKTNCDIAIGTTAGIGRG 112 (165)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeccccCCc
Confidence 36778888888888777788889998853
No 40
>PF09016 Pas_Saposin: Pas factor saposin fold; InterPro: IPR015106 Members of this entry adopt a compact structure comprising five alpha helices. Charged and polar residues are exposed mostly on the surface, while most of the hydrophobic residues are buried inside the hydrophobic core of the helical bundle. The precise function of this domain is unknown, but it is has been shown to induce secretion of periplasmic proteins, especially collagenase []. ; PDB: 2B8I_A.
Probab=25.56 E-value=54 Score=21.08 Aligned_cols=14 Identities=14% Similarity=0.332 Sum_probs=10.0
Q ss_pred HHHHHHHHHhhCce
Q psy16216 105 EEIRAAVLSKTQFH 118 (129)
Q Consensus 105 ~~iR~~I~~~lglt 118 (129)
.+||+.+|++++|+
T Consensus 21 A~IRQ~LYeqLdLp 34 (76)
T PF09016_consen 21 AQIRQNLYEQLDLP 34 (76)
T ss_dssp HHHHHHHHHHH---
T ss_pred HHHHHHHHHHcCCc
Confidence 57999999999975
No 41
>COG4019 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.55 E-value=49 Score=23.88 Aligned_cols=32 Identities=28% Similarity=0.342 Sum_probs=26.9
Q ss_pred HHHHHHHHHhcc-hhhhhcccchhhhhccHHHH
Q psy16216 5 GREVIAVLSEFS-NIVERASIDEAYIDLTDVVH 36 (129)
Q Consensus 5 S~~I~~il~~~~-p~ve~~SiDEaylDlT~~v~ 36 (129)
-+.|.+++++|+ +..|.+-||--|-|+|.+..
T Consensus 49 ~~aindvlrrf~l~Eaeml~~~T~~ADlTrmPA 81 (156)
T COG4019 49 FKAINDVLRRFCLAEAEMLDIDTRFADLTRMPA 81 (156)
T ss_pred HHHHHHHHHHhccchHHHhcCccchhhcccChH
Confidence 356888999987 58999999999999997653
No 42
>PF06973 DUF1297: Domain of unknown function (DUF1297); InterPro: IPR009720 The last two steps of de novo purine biosynthesis are: i) conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR) ii) conversion of FAICAR to inosine5'-monophopsphate (IMP) In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH []. Archaea do not appear to posses PurH, however, and perform these reactions by a different mechanism []. In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species [, ]. This entry represents the C-terminal domain of PurP, which is homologous to the ATP-GRASP fold and thus may be involved in ATP-binding. It is almost always found in association with IPR010672 from INTERPRO.; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0006188 IMP biosynthetic process; PDB: 2R85_B 2R87_E 2R84_A 2R86_A 2PBZ_B 2R7L_A 2R7N_A 2R7K_A 2R7M_A.
Probab=24.31 E-value=69 Score=24.31 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy16216 96 ELAIAGVIVEEIRAAVLS 113 (129)
Q Consensus 96 ~l~~aa~ia~~iR~~I~~ 113 (129)
.+..|.+||.+||.++.+
T Consensus 163 pms~GrRIA~EIk~A~e~ 180 (188)
T PF06973_consen 163 PMSMGRRIAREIKEAIEE 180 (188)
T ss_dssp ---HHHHHHHHHHHHHHT
T ss_pred CcchhHHHHHHHHHHHHc
Confidence 467899999999999865
No 43
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=23.08 E-value=25 Score=28.77 Aligned_cols=26 Identities=35% Similarity=0.507 Sum_probs=16.1
Q ss_pred HHHHHHHhcchhhhhcccchhhhhccH
Q psy16216 7 EVIAVLSEFSNIVERASIDEAYIDLTD 33 (129)
Q Consensus 7 ~I~~il~~~~p~ve~~SiDEaylDlT~ 33 (129)
+|.+++..... --.+=|||||+|.+.
T Consensus 166 ~l~~l~~~~~~-~~~vVvDEAY~eF~~ 191 (356)
T COG0079 166 ELRALLEALPE-GGLVVIDEAYIEFSP 191 (356)
T ss_pred HHHHHHHhCCC-CcEEEEeCchhhcCC
Confidence 34444444332 234568999999988
No 44
>PRK09438 nudB dihydroneopterin triphosphate pyrophosphatase; Provisional
Probab=23.06 E-value=74 Score=21.92 Aligned_cols=20 Identities=15% Similarity=0.023 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHhhCceeee
Q psy16216 102 VIVEEIRAAVLSKTQFHCSA 121 (129)
Q Consensus 102 ~ia~~iR~~I~~~lgltcSa 121 (129)
....-+++.+++|||+++.+
T Consensus 45 s~~~aa~REl~EEtGl~~~~ 64 (148)
T PRK09438 45 TPAQTAIREVKEETGIDVLA 64 (148)
T ss_pred CHHHHHHHHHHHHhCcCccc
Confidence 35566788899999999843
No 45
>COG1353 Predicted CRISPR-associated polymerase [Defense mechanisms]
Probab=22.97 E-value=79 Score=28.98 Aligned_cols=35 Identities=23% Similarity=0.172 Sum_probs=19.9
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHhhCceeeecccC
Q psy16216 89 ENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAH 125 (129)
Q Consensus 89 ~~~~~~~~l~~aa~ia~~iR~~I~~~lgltcSaGIa~ 125 (129)
.-|+++ +..|.++....+.-.-....+|+||||..
T Consensus 600 g~~d~v--ld~a~el~~~F~~~~~~~~~~t~SaGi~i 634 (799)
T COG1353 600 GPWDDV--LDFAKELRELFSEFTGKNPKLTLSAGIVI 634 (799)
T ss_pred ccHHHH--HHHHHHHHHHHHHHhcCCCceeEEEEEEE
Confidence 457775 44444444444444444444599999863
No 46
>PLN02177 glycerol-3-phosphate acyltransferase
Probab=22.92 E-value=77 Score=27.39 Aligned_cols=21 Identities=14% Similarity=0.311 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHhhCceee
Q psy16216 100 AGVIVEEIRAAVLSKTQFHCS 120 (129)
Q Consensus 100 aa~ia~~iR~~I~~~lgltcS 120 (129)
..++|.++++.|.+++|+.|+
T Consensus 452 ~~evAn~Vq~~i~~~lg~~~t 472 (497)
T PLN02177 452 PIEVANYIQRVLAGTLGFECT 472 (497)
T ss_pred HHHHHHHHHHHHHHhhCceec
Confidence 468999999999999999997
No 47
>PF02552 CO_dh: CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit; InterPro: IPR003704 Carbon monoxide dehydrogenase (Cdh) from Methanosarcina mazei (Methanosarcina frisia) Go1 is a Ni2+-, Fe2+-, and S2-containing alpha2beta2 heterotetramer []. The CO dehydrogenase enzyme complex from Methanosarcina thermophila contains a corrinoid/iron-sulphur enzyme composed of two subunits (delta and gamma) []. This family consists of carbon monoxide dehydrogenase I/II beta subunit 1.2.99.2 from EC and CO dehydrogenase (acetyl-CoA synthase epsilon subunit).; GO: 0019385 methanogenesis, from acetate; PDB: 3CF4_G 1YTL_B.
Probab=21.17 E-value=58 Score=24.11 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhcchhhhhcccchhhh
Q psy16216 4 AGREVIAVLSEFSNIVERASIDEAYI 29 (129)
Q Consensus 4 ~S~~I~~il~~~~p~ve~~SiDEayl 29 (129)
...+++.+|+.|+|.+-.++||+.|-
T Consensus 117 ya~~~Ls~LK~ftp~~~t~~~~~~yh 142 (167)
T PF02552_consen 117 YANQVLSILKHFTPCLKTISCDRYYH 142 (167)
T ss_dssp HHHHHHHHHHHH-TT-EEEE-SSS--
T ss_pred HHHHHHHHHhccCCceEEEEeccccC
Confidence 46788999999999999999998884
No 48
>cd03675 Nudix_Hydrolase_2 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability,
Probab=20.62 E-value=89 Score=20.90 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHhhCceeee
Q psy16216 102 VIVEEIRAAVLSKTQFHCSA 121 (129)
Q Consensus 102 ~ia~~iR~~I~~~lgltcSa 121 (129)
....-+.+.+++|+|++++.
T Consensus 38 s~~~aa~REl~EEtGl~~~~ 57 (134)
T cd03675 38 SLIEAAVRETLEETGWHVEP 57 (134)
T ss_pred CHHHHHHHHHHHHHCccccc
Confidence 35566777889999999865
No 49
>PF13592 HTH_33: Winged helix-turn helix
Probab=20.39 E-value=1.1e+02 Score=18.23 Aligned_cols=17 Identities=24% Similarity=0.219 Sum_probs=12.0
Q ss_pred HHHHHHHHHHhhCceee
Q psy16216 104 VEEIRAAVLSKTQFHCS 120 (129)
Q Consensus 104 a~~iR~~I~~~lgltcS 120 (129)
+.+|+.-|.+++|.+.|
T Consensus 7 ~~~i~~~I~~~fgv~ys 23 (60)
T PF13592_consen 7 LKEIAAYIEEEFGVKYS 23 (60)
T ss_pred HHHHHHHHHHHHCCEEc
Confidence 34566777788887776
Done!