Query 040790
Match_columns 231
No_of_seqs 113 out of 219
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 11:50:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040790.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040790hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14144 DOG1: Seed dormancy c 100.0 1.4E-36 3.1E-41 227.0 7.6 80 19-100 1-80 (80)
2 PF13801 Metal_resist: Heavy-m 97.2 0.006 1.3E-07 46.4 10.4 81 123-203 41-124 (125)
3 PRK12750 cpxP periplasmic repr 96.7 0.081 1.7E-06 44.8 13.7 98 123-220 52-160 (170)
4 COG3678 CpxP P pilus assembly/ 96.5 0.044 9.6E-07 46.1 11.3 85 123-210 57-144 (160)
5 PRK10455 periplasmic protein; 95.4 0.24 5.2E-06 41.7 10.5 83 123-207 56-140 (161)
6 PF07813 LTXXQ: LTXXQ motif fa 95.0 0.15 3.2E-06 37.9 7.4 78 123-205 14-96 (100)
7 PRK12751 cpxP periplasmic stre 94.9 0.66 1.4E-05 39.1 11.9 94 123-218 56-151 (162)
8 PRK10363 cpxP periplasmic repr 94.9 0.24 5.2E-06 42.0 9.2 83 123-207 50-134 (166)
9 PRK14563 ribosome modulation f 61.6 3.6 7.8E-05 28.8 0.6 15 76-91 33-47 (55)
10 PRK11546 zraP zinc resistance 44.8 1.8E+02 0.0039 24.1 10.7 70 119-188 39-111 (143)
11 COG3130 Rmf Ribosome modulatio 44.2 8 0.00017 26.7 0.1 17 76-92 32-48 (55)
12 PF14644 DUF4456: Domain of un 44.0 35 0.00076 29.5 4.2 40 4-46 95-134 (208)
13 PHA03395 p10 fibrous body prot 42.2 1.3E+02 0.0029 22.9 6.5 58 138-199 8-67 (87)
14 PF11239 DUF3040: Protein of u 39.8 27 0.0006 25.7 2.5 30 123-152 2-31 (82)
15 PF06698 DUF1192: Protein of u 39.3 85 0.0019 22.2 4.8 35 118-152 15-50 (59)
16 PF13586 DDE_Tnp_1_2: Transpos 38.7 14 0.0003 27.2 0.7 19 72-90 44-62 (88)
17 PF05531 NPV_P10: Nucleopolyhe 37.9 1.7E+02 0.0036 21.7 6.8 58 138-199 8-67 (75)
18 PF07889 DUF1664: Protein of u 36.1 2.3E+02 0.0051 22.9 8.0 18 81-98 21-38 (126)
19 PF04957 RMF: Ribosome modulat 35.9 7.3 0.00016 27.3 -1.1 14 77-90 33-46 (55)
20 PF11459 DUF2893: Protein of u 35.5 99 0.0021 22.6 4.7 42 172-213 20-61 (69)
21 PLN02796 D-glycerate 3-kinase 35.0 1E+02 0.0023 29.1 6.0 43 10-58 278-320 (347)
22 TIGR00153 conserved hypothetic 34.0 1.3E+02 0.0027 25.8 6.1 55 146-200 23-78 (216)
23 PF00589 Phage_integrase: Phag 33.6 19 0.00041 28.1 0.8 20 81-100 28-47 (173)
24 PHA03386 P10 fibrous body prot 32.0 1.8E+02 0.0039 22.6 5.8 52 139-199 10-61 (94)
25 PF10234 Cluap1: Clusterin-ass 29.1 2.2E+02 0.0048 26.0 6.9 61 131-193 159-219 (267)
26 PF14361 RsbRD_N: RsbT co-anta 28.8 2.6E+02 0.0056 21.1 7.3 39 67-106 56-100 (105)
27 PLN03046 D-glycerate 3-kinase; 28.4 1.1E+02 0.0025 30.0 5.2 44 9-58 389-432 (460)
28 TIGR02302 aProt_lowcomp conser 28.0 7.6E+02 0.017 26.3 12.8 124 22-193 510-646 (851)
29 PF04678 DUF607: Protein of un 26.1 2.6E+02 0.0056 23.5 6.5 37 123-160 50-86 (180)
30 PF05227 CHASE3: CHASE3 domain 25.9 3E+02 0.0064 20.9 6.9 47 4-56 38-84 (138)
31 PF01865 PhoU_div: Protein of 25.0 2.5E+02 0.0053 23.6 6.3 36 166-201 40-76 (214)
32 COG3407 MVD1 Mevalonate pyroph 25.0 1.4E+02 0.0031 28.0 5.1 45 7-58 203-247 (329)
33 cd00068 GGL G protein gamma su 25.0 1.4E+02 0.003 20.6 3.8 46 15-74 2-47 (57)
34 PF10552 ORF6C: ORF6C domain; 23.9 97 0.0021 24.2 3.3 21 76-96 93-113 (116)
35 COG4323 Predicted membrane pro 22.9 18 0.00038 27.9 -1.1 70 4-102 10-90 (105)
36 cd00223 TOPRIM_TopoIIB_SPO TOP 22.7 1.2E+02 0.0026 24.7 3.8 38 82-140 90-127 (160)
37 PF10925 DUF2680: Protein of u 22.5 2.3E+02 0.005 19.8 4.6 16 124-139 1-16 (59)
38 COG1510 Predicted transcriptio 22.2 2.9E+02 0.0062 23.8 5.9 63 8-70 97-170 (177)
39 TIGR03319 YmdA_YtgF conserved 22.1 7.8E+02 0.017 24.4 10.9 46 166-211 111-158 (514)
40 PRK10626 hypothetical protein; 21.9 4.3E+02 0.0094 23.8 7.3 57 123-180 64-128 (239)
41 PF03371 PRP38: PRP38 family; 21.6 75 0.0016 26.9 2.4 14 89-102 62-75 (172)
42 PRK15366 type III secretion sy 21.1 1.9E+02 0.0041 21.7 4.1 27 122-148 38-64 (80)
43 PF11351 DUF3154: Protein of u 21.0 2.1E+02 0.0046 22.7 4.7 13 84-96 57-69 (123)
44 KOG2202 U2 snRNP splicing fact 20.9 1.5E+02 0.0033 27.0 4.2 61 4-76 76-136 (260)
No 1
>PF14144 DOG1: Seed dormancy control
Probab=100.00 E-value=1.4e-36 Score=227.00 Aligned_cols=80 Identities=44% Similarity=0.926 Sum_probs=75.0
Q ss_pred HHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHHHhhhhcchhhhccCCCCchHHHHHHHhcCCchhHHHHHHH
Q 040790 19 QLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVKSAEAQRDVFNVFAAPWASSLERSLHWIAGWRPTTVFHLVY 98 (231)
Q Consensus 19 ~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~l~Ll~ 98 (231)
++++|||++++++ ..+|++|+.+|++|++||++||++|+.||++|||++|+|+|+||+||||+||||||||++|+|||
T Consensus 1 ~~l~eLr~al~~~--~~~~~~L~~lV~~~~~Hy~~y~~~K~~aa~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~~~ll~ 78 (80)
T PF14144_consen 1 RQLNELRAALQSH--ADSDDELRSLVDKVMSHYDEYYRAKSAAAKADVFHLLSPPWKSPLERCFLWIGGWRPSELFKLLY 78 (80)
T ss_pred CcHHHHHHHHHhc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHhCCCCCCHHHHHHHHHhcCCHHHHHHHHh
Confidence 4789999999833 34799999999999999999999999999999999999999999999999999999999999999
Q ss_pred hh
Q 040790 99 TE 100 (231)
Q Consensus 99 s~ 100 (231)
|+
T Consensus 79 s~ 80 (80)
T PF14144_consen 79 SQ 80 (80)
T ss_pred cC
Confidence 74
No 2
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=97.19 E-value=0.006 Score=46.39 Aligned_cols=81 Identities=20% Similarity=0.252 Sum_probs=70.0
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhhcCCC---chhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCH
Q 040790 123 DLSPSQFRRVSELQCETVKEENAITDELSEWQDGASELVGDC---SASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTT 199 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~g~~---~~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp 199 (231)
+||++|..+|..+......+-..+-+.+......+...+... ...+...++.+...-.+....|.+++.++..+|||
T Consensus 41 ~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~~~l~~~~~~~~~~~~~~Ltp 120 (125)
T PF13801_consen 41 NLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAAPPPDEAAIEALLEEIREAQAELRQERLEHLLEIRAVLTP 120 (125)
T ss_dssp -TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-G
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 599999999999999999999999999999999998888433 23467788888999999999999999999999999
Q ss_pred HHHH
Q 040790 200 QQAV 203 (231)
Q Consensus 200 ~Qaa 203 (231)
.|=+
T Consensus 121 eQR~ 124 (125)
T PF13801_consen 121 EQRA 124 (125)
T ss_dssp GGHH
T ss_pred HHhC
Confidence 9855
No 3
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=96.67 E-value=0.081 Score=44.85 Aligned_cols=98 Identities=16% Similarity=0.148 Sum_probs=62.4
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHH--------HHHHHHHHHhhhhhhcCC--Cchh-HHHHHHHHHHHHHHHhHHHHHHHH
Q 040790 123 DLSPSQFRRVSELQCETVKEENA--------ITDELSEWQDGASELVGD--CSAS-VDEKIRLLVSIVQKADDLRLRTVR 191 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~a--------Ls~~ma~lQ~slad~~g~--~~~~-~~~kl~~L~~~l~~AD~LR~~TL~ 191 (231)
+||++|...|..++...+.+=.+ ..+.|....+.+.+.+.+ .+.+ +.+-.+.+...-.+.---|.++.+
T Consensus 52 ~LTdeQk~qik~i~~~~r~~~k~~~~~~r~~~~~~m~a~~~~~~~Ll~a~~FDeaavral~~~~~~~~~e~~v~~~~~~~ 131 (170)
T PRK12750 52 DLTDAQKEQLKEMREANRAEMKAKYSGNREQSHAEMKAHHAKVQALVLADDFDEAAANDLAKQMVEKQVERRVKMLEKRH 131 (170)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 59999999999998777764333 345555555555555532 2222 223223333332333334677899
Q ss_pred HHhhhcCHHHHHHHHHHHHHHHHHHhhcc
Q 040790 192 RVVDLLTTQQAVEFLIAAAELQFGVRKWG 220 (231)
Q Consensus 192 ~~~~iLtp~Qaa~fL~A~~e~~~~lr~~g 220 (231)
++..||||-|=+.|-.-..+.....++-+
T Consensus 132 ~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 132 QMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999888666655555544
No 4
>COG3678 CpxP P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]
Probab=96.55 E-value=0.044 Score=46.11 Aligned_cols=85 Identities=19% Similarity=0.236 Sum_probs=62.3
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhhcCC---CchhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCH
Q 040790 123 DLSPSQFRRVSELQCETVKEENAITDELSEWQDGASELVGD---CSASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTT 199 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~g~---~~~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp 199 (231)
+||++|..+|.++...-+ .+..+-+..-..++-+.+.+ +...+....+.++..-.+.+.+|.++-.++..||||
T Consensus 57 ~lT~~Qrqqi~~i~~~~~---~a~~~~~~~~r~~l~~li~a~~~D~aka~a~~~~m~~~~~~~~~~r~k~~~~m~~vLTP 133 (160)
T COG3678 57 DLTRAQRQQIRDLMQAQR---RAQREQLRSKRRALHELIAADQFDEAKARAQAEKMENQRQALRELRVKSDNQMYQVLTP 133 (160)
T ss_pred cccHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCH
Confidence 599999999999887766 33333333344444444422 223567888899999999999999999999999999
Q ss_pred HHHHHHHHHHH
Q 040790 200 QQAVEFLIAAA 210 (231)
Q Consensus 200 ~Qaa~fL~A~~ 210 (231)
.|.+.|=--.+
T Consensus 134 EQr~~l~~~~~ 144 (160)
T COG3678 134 EQRAKLQELLA 144 (160)
T ss_pred HHHHHHHHHHH
Confidence 99977654433
No 5
>PRK10455 periplasmic protein; Reviewed
Probab=95.37 E-value=0.24 Score=41.66 Aligned_cols=83 Identities=13% Similarity=0.171 Sum_probs=55.1
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHHH-HHHHHHHhhhhhhcCCCc-hhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCHH
Q 040790 123 DLSPSQFRRVSELQCETVKEENAIT-DELSEWQDGASELVGDCS-ASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTTQ 200 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aLs-~~ma~lQ~slad~~g~~~-~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp~ 200 (231)
+||++|..+|..|.+..+..-...+ ++...++.-++. +..+ ..+...++.+...-.+.-..|.++-.+|..||||-
T Consensus 56 ~LT~~Qrqqir~im~~~r~~~~~~~~~~r~~l~~li~a--d~FDeaavra~~~k~~~~~~~~~~~~~~~~~qiy~vLTPE 133 (161)
T PRK10455 56 NLTDAQKQQIRDIMKAQRDQMKRPPLEERRAMHDIIAS--DTFDKAKAEAQITKMEAQRKARMLAHMETQNKIYNVLTPE 133 (161)
T ss_pred CCCHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHcc--CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHH
Confidence 4999999999999877666533332 333444432211 1122 23555566666666666667889999999999999
Q ss_pred HHHHHHH
Q 040790 201 QAVEFLI 207 (231)
Q Consensus 201 Qaa~fL~ 207 (231)
|-+.|=.
T Consensus 134 Qr~q~~~ 140 (161)
T PRK10455 134 QKKQFNA 140 (161)
T ss_pred HHHHHHH
Confidence 9998764
No 6
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=94.98 E-value=0.15 Score=37.88 Aligned_cols=78 Identities=13% Similarity=0.164 Sum_probs=48.4
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHH---HHHHHHHHhhhhhhcCCCchhHHHHH--HHHHHHHHHHhHHHHHHHHHHhhhc
Q 040790 123 DLSPSQFRRVSELQCETVKEENAI---TDELSEWQDGASELVGDCSASVDEKI--RLLVSIVQKADDLRLRTVRRVVDLL 197 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aL---s~~ma~lQ~slad~~g~~~~~~~~kl--~~L~~~l~~AD~LR~~TL~~~~~iL 197 (231)
+||++|...+..|....+..-..+ .+.+.++.+ .......+.... +.+...-.+.-..|..+...+..||
T Consensus 14 ~LT~eQ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL 88 (100)
T PF07813_consen 14 NLTDEQKAKWRAIRQAMKAKMKPLKAMREQLRALRD-----PSFDEAAPEALAAMAEMMELRAEMMEERAKAQHALYAVL 88 (100)
T ss_dssp --THHHHHHHHHHHHHHCTTS------HHHHHHHHH-----SS--HHHHHHHH--HHCHHHHHHHHHHHHHHHHHHHTTS
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhhcccHHHHHHhcc-----ccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 399999999999998888777776 233333323 111112222222 5666666666677889999999999
Q ss_pred CHHHHHHH
Q 040790 198 TTQQAVEF 205 (231)
Q Consensus 198 tp~Qaa~f 205 (231)
||-|=+.|
T Consensus 89 t~eQk~~~ 96 (100)
T PF07813_consen 89 TPEQKEKF 96 (100)
T ss_dssp -HHHHHHH
T ss_pred CHHHHHHH
Confidence 99998776
No 7
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=94.93 E-value=0.66 Score=39.14 Aligned_cols=94 Identities=11% Similarity=0.057 Sum_probs=62.6
Q ss_pred CCCHHHHHHHHHHhHHHHHHHH-HHHHHHHHHHhhhhhhcCCCc-hhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCHH
Q 040790 123 DLSPSQFRRVSELQCETVKEEN-AITDELSEWQDGASELVGDCS-ASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTTQ 200 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~-aLs~~ma~lQ~slad~~g~~~-~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp~ 200 (231)
+||++|...|-.+....+.... .--.+++.++..+..- +.+ ..+.+.++.+...-..----+.++..++..+|||-
T Consensus 56 ~LTd~QR~qmr~im~~~r~~~~~~~~~~~~~m~~Li~Ad--~FDeaAvra~~~kma~~~~e~~v~~~~~~~qmy~lLTPE 133 (162)
T PRK12751 56 NLTEQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLITAD--KFDEAAVRAQAEKMSQNQIERHVEMAKVRNQMYNLLTPE 133 (162)
T ss_pred CCCHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHH
Confidence 4999999999999888776532 1122444444433332 222 33555566665555555557788999999999999
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 040790 201 QAVEFLIAAAELQFGVRK 218 (231)
Q Consensus 201 Qaa~fL~A~~e~~~~lr~ 218 (231)
|-+.|---.-+-...+++
T Consensus 134 Qra~l~~~~e~r~~~~~~ 151 (162)
T PRK12751 134 QKEALNKKHQERIEKLQQ 151 (162)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999997766666655555
No 8
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=94.91 E-value=0.24 Score=42.00 Aligned_cols=83 Identities=12% Similarity=0.117 Sum_probs=54.4
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHHH-HHHHHHHhhhhhhcCCCc-hhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCHH
Q 040790 123 DLSPSQFRRVSELQCETVKEENAIT-DELSEWQDGASELVGDCS-ASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTTQ 200 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aLs-~~ma~lQ~slad~~g~~~-~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp~ 200 (231)
+||++|...|.+|.+.-+.+.+.++ .+++.++.-+..- ..+ ..+...++.+...=.+.-=-|.++-++|..||||-
T Consensus 50 dLTdaQRqQmRdLm~~~r~~~~~~~~~er~amh~LI~ad--~FDEaavra~a~kma~~~~e~~Vem~k~~nqmy~lLTPE 127 (166)
T PRK10363 50 SLTEHQRQQMRDLMQQARHEQPPVNVSEMETMHRLVTAE--NFDENAVRAQAEKMAQEQVARQVEMAKVRNQMYRLLTPE 127 (166)
T ss_pred CCCHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHH
Confidence 4999999999999988887655443 2455554222211 122 33445555554444444445778899999999999
Q ss_pred HHHHHHH
Q 040790 201 QAVEFLI 207 (231)
Q Consensus 201 Qaa~fL~ 207 (231)
|-+.|=-
T Consensus 128 QKaq~~~ 134 (166)
T PRK10363 128 QQAVLNE 134 (166)
T ss_pred HHHHHHH
Confidence 9999843
No 9
>PRK14563 ribosome modulation factor; Provisional
Probab=61.58 E-value=3.6 Score=28.83 Aligned_cols=15 Identities=40% Similarity=1.035 Sum_probs=10.7
Q ss_pred chHHHHHHHhcCCchh
Q 040790 76 SSLERSLHWIAGWRPT 91 (231)
Q Consensus 76 sp~Er~flWiGG~RPS 91 (231)
++--++ .||||||--
T Consensus 33 ~~~~r~-~Wl~GWReg 47 (55)
T PRK14563 33 TLDARS-QWLGGWREA 47 (55)
T ss_pred CcHHHH-HHHHHHHHH
Confidence 444455 899999954
No 10
>PRK11546 zraP zinc resistance protein; Provisional
Probab=44.80 E-value=1.8e+02 Score=24.11 Aligned_cols=70 Identities=14% Similarity=0.215 Sum_probs=44.8
Q ss_pred CCCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhhcCCC--chh-HHHHHHHHHHHHHHHhHHHHH
Q 040790 119 GDLGDLSPSQFRRVSELQCETVKEENAITDELSEWQDGASELVGDC--SAS-VDEKIRLLVSIVQKADDLRLR 188 (231)
Q Consensus 119 ~~l~~Ls~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~g~~--~~~-~~~kl~~L~~~l~~AD~LR~~ 188 (231)
+...+||++|...++.|+++-..+=..|-+.|-.-+..+-....+. +.. +...-.++..+=.+-+.+|.+
T Consensus 39 ~~~~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~~ 111 (143)
T PRK11546 39 QNAAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRVK 111 (143)
T ss_pred cccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556899999999999998888877777777777666666655322 122 333333444444455555543
No 11
>COG3130 Rmf Ribosome modulation factor [Translation, ribosomal structure and biogenesis]
Probab=44.19 E-value=8 Score=26.72 Aligned_cols=17 Identities=29% Similarity=0.970 Sum_probs=12.2
Q ss_pred chHHHHHHHhcCCchhH
Q 040790 76 SSLERSLHWIAGWRPTT 92 (231)
Q Consensus 76 sp~Er~flWiGG~RPS~ 92 (231)
+.++.--.|+||||--.
T Consensus 32 q~~~~Rs~WLgGWRea~ 48 (55)
T COG3130 32 QTLNQRSQWLGGWREAM 48 (55)
T ss_pred cCchHHHHHHHHHHHHh
Confidence 34555568999999654
No 12
>PF14644 DUF4456: Domain of unknown function (DUF4456)
Probab=44.03 E-value=35 Score=29.47 Aligned_cols=40 Identities=30% Similarity=0.390 Sum_probs=34.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHH
Q 040790 4 SSFSSFYSTWFEQLNQLVQQLSAAARPPTTYDQHQDLEKLVAK 46 (231)
Q Consensus 4 ~~F~~~y~~W~~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~ 46 (231)
..|..++..|...-+.+..+||-.|. +|....+|..|.+.
T Consensus 95 ~~f~~~~~~~~~~k~~h~~~LrP~Lg---hP~~~~eL~~L~~~ 134 (208)
T PF14644_consen 95 EEFEQQQKQWEQQKDQHEQQLRPNLG---HPDNRQELESLCER 134 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcCC---CCCCHHHHHHHHHH
Confidence 46999999999999999999999996 45567889888764
No 13
>PHA03395 p10 fibrous body protein; Provisional
Probab=42.24 E-value=1.3e+02 Score=22.92 Aligned_cols=58 Identities=14% Similarity=0.289 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCCC--chhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCH
Q 040790 138 ETVKEENAITDELSEWQDGASELVGDC--SASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTT 199 (231)
Q Consensus 138 ~t~~~E~aLs~~ma~lQ~slad~~g~~--~~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp 199 (231)
-++.+-.++++....+|+.+.+.-+.- -.++.++++++-.-+...+ .++..|.+||+|
T Consensus 8 ~Ir~dIkavd~KVdalQ~~V~~l~~nlpdv~~l~~kLdaq~~~Ltti~----tkv~~I~diLnp 67 (87)
T PHA03395 8 LIRQDIKAVSDKVDALQAAVDDVRANLPDVTEINEKLDAQSASLDTIS----SAVDNITDILNP 67 (87)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHhcCCcHHHHHHHHHhHHHHHHHHH----HHHHHHHHccCC
Confidence 367777889999999999888875321 1345677877776665444 567778888887
No 14
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=39.80 E-value=27 Score=25.65 Aligned_cols=30 Identities=20% Similarity=0.322 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 040790 123 DLSPSQFRRVSELQCETVKEENAITDELSE 152 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aLs~~ma~ 152 (231)
|||++..+.++++++....+.+.+...|..
T Consensus 2 ~LSe~E~r~L~eiEr~L~~~DP~fa~~l~~ 31 (82)
T PF11239_consen 2 PLSEHEQRRLEEIERQLRADDPRFAARLRS 31 (82)
T ss_pred CCCHHHHHHHHHHHHHHHhcCcHHHHHhcc
Confidence 689999999999999999999999999887
No 15
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=39.34 E-value=85 Score=22.20 Aligned_cols=35 Identities=29% Similarity=0.367 Sum_probs=29.1
Q ss_pred CCCCCCCCHHHHH-HHHHHhHHHHHHHHHHHHHHHH
Q 040790 118 TGDLGDLSPSQFR-RVSELQCETVKEENAITDELSE 152 (231)
Q Consensus 118 ~~~l~~Ls~~Ql~-~i~~Lq~~t~~~E~aLs~~ma~ 152 (231)
+-+|+.||-..|. +|..|+.++.+.|.++...-+.
T Consensus 15 g~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~K~a~ 50 (59)
T PF06698_consen 15 GEDLSLLSVEELEERIALLEAEIARLEAAIAKKSAS 50 (59)
T ss_pred CCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578889998887 5999999999999999876554
No 16
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=38.75 E-value=14 Score=27.15 Aligned_cols=19 Identities=21% Similarity=0.466 Sum_probs=15.6
Q ss_pred CCCCchHHHHHHHhcCCch
Q 040790 72 APWASSLERSLHWIAGWRP 90 (231)
Q Consensus 72 ~~W~sp~Er~flWiGG~RP 90 (231)
.+.+.-.||+|-||.+||-
T Consensus 44 ~~~Rw~VEr~f~wlk~~Rr 62 (88)
T PF13586_consen 44 YKRRWVVERTFAWLKRFRR 62 (88)
T ss_pred hccceehhhhhHHHHHcCc
Confidence 4555579999999999984
No 17
>PF05531 NPV_P10: Nucleopolyhedrovirus P10 protein; InterPro: IPR008702 This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra [].; GO: 0019028 viral capsid
Probab=37.86 E-value=1.7e+02 Score=21.75 Aligned_cols=58 Identities=14% Similarity=0.266 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCCC--chhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCH
Q 040790 138 ETVKEENAITDELSEWQDGASELVGDC--SASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTT 199 (231)
Q Consensus 138 ~t~~~E~aLs~~ma~lQ~slad~~g~~--~~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp 199 (231)
-+++.-.++++.+..+|..+.+.-..- -.++..|++++..-+..=+. ++..+.+||+|
T Consensus 8 ~Ir~dIk~vd~KVdaLq~~V~~l~~~~~~v~~l~~klDa~~~~l~~l~~----~V~~I~~iL~~ 67 (75)
T PF05531_consen 8 VIRQDIKAVDDKVDALQTQVDDLESNLPDVTELNKKLDAQSAQLTTLNT----KVNEIQDILNP 67 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHH----HHHHHHHHhCC
Confidence 356667788888888888886654221 13467788777666655442 77788888885
No 18
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=36.15 E-value=2.3e+02 Score=22.90 Aligned_cols=18 Identities=17% Similarity=0.606 Sum_probs=12.9
Q ss_pred HHHHhcCCchhHHHHHHH
Q 040790 81 SLHWIAGWRPTTVFHLVY 98 (231)
Q Consensus 81 ~flWiGG~RPS~~l~Ll~ 98 (231)
+++|.=||.=|.+.=+-.
T Consensus 21 ~Y~wwKGws~sD~M~vTr 38 (126)
T PF07889_consen 21 GYMWWKGWSFSDLMFVTR 38 (126)
T ss_pred eeeeecCCchhHHHHHHH
Confidence 478888998887655443
No 19
>PF04957 RMF: Ribosome modulation factor; InterPro: IPR007040 This entry contains ribosome modulation factors (RMF). They associate with 70s ribosomes and converts them to a dimeric form (100S ribosomes) which appear during the transition from the exponential growth phase to the stationary phase of Escherichia colicells [, ]. It has been proposed that RMF mediates the formation of a 'storage ribosome', the 100S particle, in stationary phase by inactivating excess ribosomes to protect them from degradation and to maintain the required balance between the concentrations of ribosomes and protein synthesis factors in order to maintain translational elongation efficiency [, ]. ; PDB: 2JRM_A 3V24_V 3V22_V.
Probab=35.88 E-value=7.3 Score=27.28 Aligned_cols=14 Identities=29% Similarity=0.942 Sum_probs=10.4
Q ss_pred hHHHHHHHhcCCch
Q 040790 77 SLERSLHWIAGWRP 90 (231)
Q Consensus 77 p~Er~flWiGG~RP 90 (231)
..+-.-.||||||-
T Consensus 33 ~~~~r~~Wl~GWre 46 (55)
T PF04957_consen 33 DGDARSQWLGGWRE 46 (55)
T ss_dssp SCHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHH
Confidence 34456799999984
No 20
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=35.50 E-value=99 Score=22.56 Aligned_cols=42 Identities=14% Similarity=0.223 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHhhhcCHHHHHHHHHHHHHHH
Q 040790 172 IRLLVSIVQKADDLRLRTVRRVVDLLTTQQAVEFLIAAAELQ 213 (231)
Q Consensus 172 l~~L~~~l~~AD~LR~~TL~~~~~iLtp~Qaa~fL~A~~e~~ 213 (231)
++....++.-..+||-+.|+++.+--|-+++.+-++.+++.+
T Consensus 20 ~e~a~~l~egL~nLrp~~lq~LL~~C~svKvkRLfl~lA~~~ 61 (69)
T PF11459_consen 20 FEEADELMEGLRNLRPRVLQELLEHCTSVKVKRLFLYLAERA 61 (69)
T ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 456677778888899999999999999999999999888865
No 21
>PLN02796 D-glycerate 3-kinase
Probab=35.05 E-value=1e+02 Score=29.09 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHH
Q 040790 10 YSTWFEQLNQLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVK 58 (231)
Q Consensus 10 y~~W~~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K 58 (231)
--+|..+|++.+. +.-. ..++|+++...|+.+|=-|..||..-
T Consensus 278 v~~WR~qQE~~l~---~~~~---~gMsde~v~~FV~~~mP~y~~y~~~l 320 (347)
T PLN02796 278 VYEWRLQAEIAMR---AKGK---PGMSDEEVADFVSRYMPAYKAYLPGL 320 (347)
T ss_pred HHHHHHHHHHHHH---HhCC---CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4579999987665 2222 24689999999999999999998865
No 22
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=33.98 E-value=1.3e+02 Score=25.81 Aligned_cols=55 Identities=9% Similarity=0.094 Sum_probs=35.7
Q ss_pred HHHHHHHHHhhhhhhcCCCchhHHHHHHHHHHHHHHHhHHHHHHHHHH-hhhcCHH
Q 040790 146 ITDELSEWQDGASELVGDCSASVDEKIRLLVSIVQKADDLRLRTVRRV-VDLLTTQ 200 (231)
Q Consensus 146 Ls~~ma~lQ~slad~~g~~~~~~~~kl~~L~~~l~~AD~LR~~TL~~~-~~iLtp~ 200 (231)
+.+.+..+.+.+-+...+.-.++......+..+=.+||.+|.+....+ ...+||.
T Consensus 23 ~~~~~~~L~~~~~~~~~~~~~~~~~~~~~I~~lE~eaD~i~~~i~~~L~~~fitP~ 78 (216)
T TIGR00153 23 VGECVQLLIKSFELLKSGNNEKDEELRKEIIEIEHEADEIKREIRLNLEKGAFLPN 78 (216)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccCcC
Confidence 444555555555444422223566777788888888999988888888 4566764
No 23
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=33.55 E-value=19 Score=28.07 Aligned_cols=20 Identities=25% Similarity=0.534 Sum_probs=14.1
Q ss_pred HHHHhcCCchhHHHHHHHhh
Q 040790 81 SLHWIAGWRPTTVFHLVYTE 100 (231)
Q Consensus 81 ~flWiGG~RPS~~l~Ll~s~ 100 (231)
.+++.+|+||++++.|=...
T Consensus 28 ~l~~~tG~R~~El~~l~~~~ 47 (173)
T PF00589_consen 28 LLLLYTGLRPSELLRLRWDD 47 (173)
T ss_dssp HHHHHHT--HHHHHT-BGGG
T ss_pred HHHHHHccchhhhhhhhhhh
Confidence 37889999999999987754
No 24
>PHA03386 P10 fibrous body protein; Provisional
Probab=32.02 E-value=1.8e+02 Score=22.55 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhcCCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCH
Q 040790 139 TVKEENAITDELSEWQDGASELVGDCSASVDEKIRLLVSIVQKADDLRLRTVRRVVDLLTT 199 (231)
Q Consensus 139 t~~~E~aLs~~ma~lQ~slad~~g~~~~~~~~kl~~L~~~l~~AD~LR~~TL~~~~~iLtp 199 (231)
++.+-.+++..+..+|+.+.+.-+.. .+++++-.-+..=+ .++..|.+||||
T Consensus 10 Ir~dIkavd~KVdaLQ~qV~dv~~n~-----~~LDa~~~qL~~l~----tkV~~Iq~iLn~ 61 (94)
T PHA03386 10 ILDAVQEVDTKVDALQTQLNGLEEDS-----QPLDGLPAQLTELD----TKVSDIQSILTG 61 (94)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHhcc-----hhhhhHHHHHHHHH----HHHHHHHHhcCc
Confidence 66777889999999999998875432 33444333332222 366777888886
No 25
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=29.15 E-value=2.2e+02 Score=25.99 Aligned_cols=61 Identities=20% Similarity=0.299 Sum_probs=38.9
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHhhhhhhcCCCchhHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 040790 131 RVSELQCETVKEENAITDELSEWQDGASELVGDCSASVDEKIRLLVSIVQKADDLRLRTVRRV 193 (231)
Q Consensus 131 ~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~~g~~~~~~~~kl~~L~~~l~~AD~LR~~TL~~~ 193 (231)
.|+++++.++.+=.++.++++..++.+...-... .++.+|++.-..=+.++. =|++||+.|
T Consensus 159 e~~~iE~~l~~ai~~~~~~~~~~~~~l~~l~~de-~~Le~KIekkk~ELER~q-KRL~sLq~v 219 (267)
T PF10234_consen 159 ELNEIEKALKEAIKAVQQQLQQTQQQLNNLASDE-ANLEAKIEKKKQELERNQ-KRLQSLQSV 219 (267)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH-HHHHHHHhc
Confidence 3566666666676777777777777776653322 567777776555555554 367777754
No 26
>PF14361 RsbRD_N: RsbT co-antagonist protein rsbRD N-terminal domain
Probab=28.78 E-value=2.6e+02 Score=21.12 Aligned_cols=39 Identities=26% Similarity=0.586 Sum_probs=27.6
Q ss_pred hhhccCCCCchHHHHHHHh------cCCchhHHHHHHHhhhhhhhh
Q 040790 67 FNVFAAPWASSLERSLHWI------AGWRPTTVFHLVYTESSTLFE 106 (231)
Q Consensus 67 ~~~~s~~W~sp~Er~flWi------GG~RPS~~l~Ll~s~~~~~~E 106 (231)
+.+..+.| .++-.++-=| =||-||+....++++-.+.++
T Consensus 56 ~d~~~~~~-~~l~~~L~~lsr~RA~Qgftpseta~fvf~LK~~l~~ 100 (105)
T PF14361_consen 56 LDLAAPEW-EELREALEELSRIRAVQGFTPSETASFVFALKRPLFE 100 (105)
T ss_pred hhccccch-HHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence 66677777 5554443333 499999999999988776655
No 27
>PLN03046 D-glycerate 3-kinase; Provisional
Probab=28.37 E-value=1.1e+02 Score=29.97 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHH
Q 040790 9 FYSTWFEQLNQLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVK 58 (231)
Q Consensus 9 ~y~~W~~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K 58 (231)
+--+|..+|++.+. +.- ...++|+++...|+..|-.|+.|+..-
T Consensus 389 ~Vy~WRlqQE~kLr---~~g---g~GMsdeqV~~FV~~YmPaY~~y~~~L 432 (460)
T PLN03046 389 CVYQWRLQAEIAMR---ADG---KPGMSDEEVMDFVSRYLPAYKAYLPTL 432 (460)
T ss_pred HHHHHHHHHHHHHH---HcC---CCCCCHHHHHHHHHHhhhHHHHHHHHH
Confidence 34468888887554 222 224689999999999999999999876
No 28
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=28.02 E-value=7.6e+02 Score=26.33 Aligned_cols=124 Identities=15% Similarity=0.221 Sum_probs=76.0
Q ss_pred HHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHHHhhhhcchhhhccCCCCchHHHHHHHhcCCchhHHHHHHHhhh
Q 040790 22 QQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVKSAEAQRDVFNVFAAPWASSLERSLHWIAGWRPTTVFHLVYTES 101 (231)
Q Consensus 22 ~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~Er~flWiGG~RPS~~l~Ll~s~~ 101 (231)
..|+.|++ .++ ||.|+..|.+..-.--++|.+....-+.++.-. +-.|..
T Consensus 510 ~aL~eAL~-~gA--sdeEI~~Lm~eLR~Am~~ym~~LAeq~~~~~~~------------------~~~~~~--------- 559 (851)
T TIGR02302 510 DALKDALE-RGA--SDEEIKQLTDKLRAAMQTYMRQLAQQLRNNPQQ------------------LARPLD--------- 559 (851)
T ss_pred HHHHHHHH-cCC--CHHHHHHHHHHHHHHHHHHHHHHHHHhhhCccc------------------ccccCC---------
Confidence 45677776 233 699999999999999999999887655554211 011110
Q ss_pred hhhhhHHHHHHhhccCCCCCCCCCHHHHHH----HHHHhHH-----HHHHHHHHHHHHHHHHhhhhhhcC----CCchhH
Q 040790 102 STLFESHIVDILRGLRTGDLGDLSPSQFRR----VSELQCE-----TVKEENAITDELSEWQDGASELVG----DCSASV 168 (231)
Q Consensus 102 ~~~~E~~~~~~l~g~~~~~l~~Ls~~Ql~~----i~~Lq~~-----t~~~E~aLs~~ma~lQ~slad~~g----~~~~~~ 168 (231)
+....+|.+.|.+ |.+|=++ .++.=..|.+.|+.+|.+=-.. | +....+
T Consensus 560 -----------------~~~~~l~~~dLq~Mmd~ieela~~G~~~~A~qlL~qlq~mmenlq~~q~~~-g~~~~~~~~~~ 621 (851)
T TIGR02302 560 -----------------PNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQLQQMMNNLQMGQPGQ-GQQMGDQSGDM 621 (851)
T ss_pred -----------------ccccccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccCcCC-CcccccchHHH
Confidence 0011244444443 3333332 2233346677788888533111 2 112357
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHH
Q 040790 169 DEKIRLLVSIVQKADDLRLRTVRRV 193 (231)
Q Consensus 169 ~~kl~~L~~~l~~AD~LR~~TL~~~ 193 (231)
...|++|..++++=..|+-+|.+..
T Consensus 622 ~q~m~~L~e~lr~QQ~L~D~tfr~~ 646 (851)
T TIGR02302 622 EQQMNKLGELMRKQQQLRDETFKLD 646 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 8899999999999999999999975
No 29
>PF04678 DUF607: Protein of unknown function, DUF607; InterPro: IPR006769 This entry represents the C-terminal domain of coiled-coil domain containing protein 109.
Probab=26.07 E-value=2.6e+02 Score=23.53 Aligned_cols=37 Identities=14% Similarity=0.122 Sum_probs=23.5
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhh
Q 040790 123 DLSPSQFRRVSELQCETVKEENAITDELSEWQDGASEL 160 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aLs~~ma~lQ~slad~ 160 (231)
+..+.+..+...|+......+.+| +.|++.+..+...
T Consensus 50 ~~~~~~~~~~~~l~~~l~~~~~el-~~le~~k~~id~~ 86 (180)
T PF04678_consen 50 NVEEYQNSRERQLRKRLEELRQEL-APLEKIKQEIDEK 86 (180)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 355666677777777777777777 4555555555443
No 30
>PF05227 CHASE3: CHASE3 domain; InterPro: IPR007891 CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE3 domains are not known at this time [].; PDB: 3VA9_A.
Probab=25.87 E-value=3e+02 Score=20.85 Aligned_cols=47 Identities=11% Similarity=0.166 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHH
Q 040790 4 SSFSSFYSTWFEQLNQLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYK 56 (231)
Q Consensus 4 ~~F~~~y~~W~~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~ 56 (231)
..|-.-|..........+.+|+..+. ++.+....++.+-.-+..|+.
T Consensus 38 ~~~l~~y~~~~~~~~~~l~~L~~l~~------~~p~q~~~l~~l~~~~~~~~~ 84 (138)
T PF05227_consen 38 PEFLEPYQEARARLEKALAQLRQLVQ------DNPEQQERLDQLEELIDQWRE 84 (138)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTT------T-HHHHHHHHHHHHHHHHHHH
T ss_pred HhhhchHHHHHHHHHHHHHHHHHHhc------CCHHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999999998885 244566667777766666663
No 31
>PF01865 PhoU_div: Protein of unknown function DUF47; InterPro: IPR018445 This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Rhizobium meliloti (Sinorhizobium meliloti) (O30498 from SWISSPROT). However, the function of this protein is also unknown (Pit stands for Phosphate transport) [].; PDB: 2OLT_C 2IIU_C 3L39_A.
Probab=25.04 E-value=2.5e+02 Score=23.64 Aligned_cols=36 Identities=14% Similarity=0.295 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHHHHHHHhHHHHHHHHHHh-hhcCHHH
Q 040790 166 ASVDEKIRLLVSIVQKADDLRLRTVRRVV-DLLTTQQ 201 (231)
Q Consensus 166 ~~~~~kl~~L~~~l~~AD~LR~~TL~~~~-~iLtp~Q 201 (231)
.++...+..+..+=.+||.+|.+....+. ..+||..
T Consensus 40 ~~~~~~~~~i~~lE~~aD~i~~~i~~~L~~~fitP~d 76 (214)
T PF01865_consen 40 EDVEELLEEIKELEHEADEIKREIREELYKSFITPFD 76 (214)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-SS-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCc
Confidence 55667777777777888888888888884 4556643
No 32
>COG3407 MVD1 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]
Probab=25.04 E-value=1.4e+02 Score=28.02 Aligned_cols=45 Identities=24% Similarity=0.426 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHH
Q 040790 7 SSFYSTWFEQLNQLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVK 58 (231)
Q Consensus 7 ~~~y~~W~~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K 58 (231)
..||..|++....++++.+.+.+ +.+...+.+..+.+..++...-
T Consensus 203 S~~y~~w~~~~~~~~~~m~~~~~-------~~Df~~i~~~~e~dsl~mHA~l 247 (329)
T COG3407 203 SPFYDAWLEHSEEDLEEMKEAIR-------EKDFEKIGELAENDSLEMHATL 247 (329)
T ss_pred ChHHHHHHHHHHHhHHHHHHHHh-------ccCHHHHHHHHHhhHHHHHHHH
Confidence 35899999999999999999997 4467778888888888776543
No 33
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=24.99 E-value=1.4e+02 Score=20.57 Aligned_cols=46 Identities=24% Similarity=0.304 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHHHhhhhcchhhhccCCC
Q 040790 15 EQLNQLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVKSAEAQRDVFNVFAAPW 74 (231)
Q Consensus 15 ~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W 74 (231)
+.+++.+..||..+. . =|.-|.++..-+..|.+.. +..|. +++|.|
T Consensus 2 ~~~~~~veqLr~el~-~--------~RikvS~a~~~l~~y~e~~---~~~Dp--ll~g~~ 47 (57)
T cd00068 2 DQLKKEVEQLRKELS-R--------ERLKVSKAAAELLKYCEQN---AENDP--LLTGPP 47 (57)
T ss_pred HHHHHHHHHHHHHHC-C--------chhhHHHHHHHHHHHHHhc---CCCCC--CCCCCC
Confidence 456778999999986 1 1556777777788888766 67785 457777
No 34
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=23.94 E-value=97 Score=24.17 Aligned_cols=21 Identities=24% Similarity=0.803 Sum_probs=17.6
Q ss_pred chHHHHHHHhcCCchhHHHHH
Q 040790 76 SSLERSLHWIAGWRPTTVFHL 96 (231)
Q Consensus 76 sp~Er~flWiGG~RPS~~l~L 96 (231)
.-+|.++-+|-+|+||..+..
T Consensus 93 kdfd~A~~~I~~W~p~~~l~~ 113 (116)
T PF10552_consen 93 KDFDEALEFINNWEPSTALKM 113 (116)
T ss_pred HHHHHHHHHHHHcCCCHHHHH
Confidence 358899999999999987753
No 35
>COG4323 Predicted membrane protein [Function unknown]
Probab=22.90 E-value=18 Score=27.91 Aligned_cols=70 Identities=26% Similarity=0.427 Sum_probs=43.6
Q ss_pred hhHHHHHHHHHHHHHHHHH-HHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHHHhhhhcchhhhccCCCCchHH---
Q 040790 4 SSFSSFYSTWFEQLNQLVQ-QLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVKSAEAQRDVFNVFAAPWASSLE--- 79 (231)
Q Consensus 4 ~~F~~~y~~W~~e~~~~l~-eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~sp~E--- 79 (231)
.+|..||.-.+.||.+-+. .|.-+- |.--|--||..+ ++|.|.=-+-
T Consensus 10 ~SFAeFYPyYl~EH~N~vcRRLH~vG-------s~LvlvcL~~~V----------------------f~~~w~wllAapv 60 (105)
T COG4323 10 KSFAEFYPYYLTEHANPVCRRLHVVG-------SSLVLVCLVLGV----------------------FRGDWRWLLAAPV 60 (105)
T ss_pred hhHHHhchHHHHhccchhHhhhhhhh-------hHHHHHHHHHHH----------------------HhcchHHHHHhhh
Confidence 5789999999999976554 332221 122233333332 3333332221
Q ss_pred --HHHHHhcCC-----chhHHHHHHHhhhh
Q 040790 80 --RSLHWIAGW-----RPTTVFHLVYTESS 102 (231)
Q Consensus 80 --r~flWiGG~-----RPS~~l~Ll~s~~~ 102 (231)
-.|.|+|-| ||.++-.=+||+||
T Consensus 61 ~GYgFAWvGHFvFEKNRPATFkyPvySlMG 90 (105)
T COG4323 61 IGYGFAWVGHFVFEKNRPATFKYPVYSLMG 90 (105)
T ss_pred hcccceeeeeeeeecCCCccccccHHHhhc
Confidence 248999987 99999999999986
No 36
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=22.73 E-value=1.2e+02 Score=24.73 Aligned_cols=38 Identities=26% Similarity=0.469 Sum_probs=28.1
Q ss_pred HHHhcCCchhHHHHHHHhhhhhhhhHHHHHHhhccCCCCCCCCCHHHHHHHHHHhHHHH
Q 040790 82 LHWIAGWRPTTVFHLVYTESSTLFESHIVDILRGLRTGDLGDLSPSQFRRVSELQCETV 140 (231)
Q Consensus 82 flWiGG~RPS~~l~Ll~s~~~~~~E~~~~~~l~g~~~~~l~~Ls~~Ql~~i~~Lq~~t~ 140 (231)
+.|+ |.+||.+.+ ++. ....+||+..+..+.+|..+..
T Consensus 90 l~~~-G~~~~d~~~-~~~-------------------~~~~~Ls~~d~~~l~~ll~~~~ 127 (160)
T cd00223 90 LRWL-GLRPSDIIR-LPD-------------------LPLLPLSERDLKRAKSLLRRPR 127 (160)
T ss_pred cEEc-cCCHHHHhh-ccc-------------------cccCCCCHHHHHHHHHHHhccc
Confidence 6676 578998876 111 2466899999999999888654
No 37
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=22.46 E-value=2.3e+02 Score=19.82 Aligned_cols=16 Identities=19% Similarity=0.210 Sum_probs=12.3
Q ss_pred CCHHHHHHHHHHhHHH
Q 040790 124 LSPSQFRRVSELQCET 139 (231)
Q Consensus 124 Ls~~Ql~~i~~Lq~~t 139 (231)
||++|...|.+|....
T Consensus 1 lT~~Qk~el~~l~~qm 16 (59)
T PF10925_consen 1 LTDQQKKELKALYKQM 16 (59)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 6899999988866543
No 38
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=22.21 E-value=2.9e+02 Score=23.82 Aligned_cols=63 Identities=13% Similarity=0.284 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCCC-------hHhHHHHHHHHHHhHHHHHHHHHhh----hhcchhhhc
Q 040790 8 SFYSTWFEQLNQLVQQLSAAARPPTTYDQ-------HQDLEKLVAKTLTHYTEYYKVKSAE----AQRDVFNVF 70 (231)
Q Consensus 8 ~~y~~W~~e~~~~l~eLr~al~~~~~~~s-------d~~L~~lV~~~~~Hy~~y~~~K~~a----A~~DV~~~~ 70 (231)
-|+++|-.+-.....-|+.++...+.... -.+....+...+.+|..||+.-..+ -..+||.++
T Consensus 97 ~f~ek~~ReId~t~e~l~k~~~e~~~~~~~~~~~~~~ke~~~~l~~~l~~~~~~~~ll~~l~e~~~~~ev~k~l 170 (177)
T COG1510 97 LFEEKWKREIDPTKEALKKLLEELNEDLDDRDLTERIKEIKSKLERLLKWSEDYYELLTRLLEFLESEEVFKYL 170 (177)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 48899999998888888887641111111 1345677888899999999976533 255777765
No 39
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=22.08 E-value=7.8e+02 Score=24.38 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHHHHHHHhHHHHHHHHHH--hhhcCHHHHHHHHHHHHH
Q 040790 166 ASVDEKIRLLVSIVQKADDLRLRTVRRV--VDLLTTQQAVEFLIAAAE 211 (231)
Q Consensus 166 ~~~~~kl~~L~~~l~~AD~LR~~TL~~~--~~iLtp~Qaa~fL~A~~e 211 (231)
..+..+...+.....+.+.++......+ +.-||.-||-..|+.-.+
T Consensus 111 ~~L~~re~eLee~~~e~~~~~~~~~~~le~~a~lt~~eak~~l~~~~~ 158 (514)
T TIGR03319 111 KELSNKEKNLDEKEEELEELIAEQREELERISGLTQEEAKEILLEEVE 158 (514)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3456677788888888888888888888 567999999988876544
No 40
>PRK10626 hypothetical protein; Provisional
Probab=21.91 E-value=4.3e+02 Score=23.75 Aligned_cols=57 Identities=14% Similarity=0.250 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHhHHHHHHHHHH----HHHHHHHHhhhhhhc----CCCchhHHHHHHHHHHHHH
Q 040790 123 DLSPSQFRRVSELQCETVKEENAI----TDELSEWQDGASELV----GDCSASVDEKIRLLVSIVQ 180 (231)
Q Consensus 123 ~Ls~~Ql~~i~~Lq~~t~~~E~aL----s~~ma~lQ~slad~~----g~~~~~~~~kl~~L~~~l~ 180 (231)
+||++|-..+.+-+...+..-+.+ +++++.--+.+.+.+ |.. +++..++..|..-++
T Consensus 64 ~L~~~Qqq~~~~Yq~~lr~~lP~i~~~a~~~l~~A~~alD~Vi~~~~G~~-snvr~rl~~l~~~l~ 128 (239)
T PRK10626 64 SLNAAQRQQAKDYQAALRQDLPWIDEGAKSRLEKARVALDKVIVQELGES-SNVRNRLTKLDAQLK 128 (239)
T ss_pred cCCHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHhccCcc-chHHHHHHHHHHHHH
Confidence 699999999999999999877755 445555555555444 443 666566665554443
No 41
>PF03371 PRP38: PRP38 family; InterPro: IPR005037 Members of this family are related to the pre mRNA splicing factor PRP38 from yeast [], therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation [].
Probab=21.64 E-value=75 Score=26.94 Aligned_cols=14 Identities=36% Similarity=0.683 Sum_probs=12.2
Q ss_pred chhHHHHHHHhhhh
Q 040790 89 RPTTVFHLVYTESS 102 (231)
Q Consensus 89 RPS~~l~Ll~s~~~ 102 (231)
|||.+|=||+.++.
T Consensus 62 ~Ps~f~CLL~KLl~ 75 (172)
T PF03371_consen 62 RPSPFFCLLYKLLQ 75 (172)
T ss_pred CCchHHHHHHHHHh
Confidence 69999999998864
No 42
>PRK15366 type III secretion system chaperone SsaE; Provisional
Probab=21.08 E-value=1.9e+02 Score=21.72 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHHHhHHHHHHHHHHHH
Q 040790 122 GDLSPSQFRRVSELQCETVKEENAITD 148 (231)
Q Consensus 122 ~~Ls~~Ql~~i~~Lq~~t~~~E~aLs~ 148 (231)
.|=|++|-.++.-|..++.++|+.|.-
T Consensus 38 ~P~sp~qYqq~t~l~ea~lqA~~IIn~ 64 (80)
T PRK15366 38 KLQDPQQYQQNTLLLEAIEQAENIINI 64 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999998753
No 43
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=21.00 E-value=2.1e+02 Score=22.71 Aligned_cols=13 Identities=23% Similarity=0.710 Sum_probs=10.4
Q ss_pred HhcCCchhHHHHH
Q 040790 84 WIAGWRPTTVFHL 96 (231)
Q Consensus 84 WiGG~RPS~~l~L 96 (231)
|..||||....-.
T Consensus 57 fv~rwRP~~~~~~ 69 (123)
T PF11351_consen 57 FVRRWRPALGWVC 69 (123)
T ss_pred cccccccHHHHHH
Confidence 9999999965553
No 44
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=20.92 E-value=1.5e+02 Score=27.01 Aligned_cols=61 Identities=11% Similarity=0.210 Sum_probs=39.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHHHhHHHHHHHHHhhhhcchhhhccCCCCc
Q 040790 4 SSFSSFYSTWFEQLNQLVQQLSAAARPPTTYDQHQDLEKLVAKTLTHYTEYYKVKSAEAQRDVFNVFAAPWAS 76 (231)
Q Consensus 4 ~~F~~~y~~W~~e~~~~l~eLr~al~~~~~~~sd~~L~~lV~~~~~Hy~~y~~~K~~aA~~DV~~~~s~~W~s 76 (231)
..|+.||+.|+.|+.....|+..--- .++-=..+|..|.-+|..--.+- + ....|.+.|.+
T Consensus 76 ~~~defyEd~f~E~~~kygEiee~~V------c~Nl~~hl~GNVYV~f~~Ee~ae--~----a~~~lnnRw~~ 136 (260)
T KOG2202|consen 76 RHEDEFYEDVFTELEDKYGEIEELNV------CDNLGDHLVGNVYVKFRSEEDAE--A----ALEDLNNRWYN 136 (260)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhh------hcccchhhhhhhhhhcccHHHHH--H----HHHHHcCcccc
Confidence 56999999999999988888776622 13333467777766665432222 2 23446677754
Done!