Query 043376
Match_columns 348
No_of_seqs 215 out of 1170
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:26:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00139 murE UDP-N-acetylmura 99.7 3.5E-17 7.6E-22 162.9 10.5 92 237-344 1-92 (460)
2 PRK14093 UDP-N-acetylmuramoyla 99.7 2.3E-16 4.9E-21 158.3 11.8 100 239-342 6-105 (479)
3 PRK10773 murF UDP-N-acetylmura 99.7 2.5E-16 5.4E-21 156.7 11.7 96 239-343 3-98 (453)
4 PF01225 Mur_ligase: Mur ligas 99.7 2.5E-18 5.4E-23 134.0 -3.8 78 263-340 1-83 (83)
5 TIGR01085 murE UDP-N-acetylmur 99.6 4.6E-16 1E-20 154.4 9.9 80 262-343 2-81 (464)
6 PRK14022 UDP-N-acetylmuramoyla 99.6 1.7E-15 3.6E-20 151.7 10.6 77 261-344 31-107 (481)
7 PRK11930 putative bifunctional 99.6 2.8E-15 6.1E-20 159.3 11.6 101 238-341 1-103 (822)
8 PRK11929 putative bifunctional 99.6 3.4E-15 7.3E-20 160.4 10.0 101 239-344 9-109 (958)
9 TIGR01143 murF UDP-N-acetylmur 99.6 3.7E-15 8.1E-20 146.3 8.8 73 269-344 1-73 (417)
10 PRK11929 putative bifunctional 99.5 5.9E-14 1.3E-18 150.9 9.8 79 261-343 523-601 (958)
11 COG0770 MurF UDP-N-acetylmuram 99.5 1.6E-13 3.5E-18 139.1 9.2 99 238-344 1-101 (451)
12 COG0769 MurE UDP-N-acetylmuram 99.0 5.6E-10 1.2E-14 113.9 6.5 79 265-345 11-89 (475)
13 PF04613 LpxD: UDP-3-O-[3-hydr 94.5 0.048 1E-06 42.2 3.7 70 262-339 3-72 (72)
14 COG1044 LpxD UDP-3-O-[3-hydrox 92.6 0.32 6.9E-06 49.0 6.8 93 238-341 2-94 (338)
15 PRK00892 lpxD UDP-3-O-[3-hydro 92.6 0.71 1.5E-05 45.3 9.0 95 238-343 1-95 (343)
16 TIGR01853 lipid_A_lpxD UDP-3-O 90.0 1.3 2.8E-05 43.6 8.0 78 256-342 10-87 (324)
17 PRK03806 murD UDP-N-acetylmura 62.0 7.7 0.00017 38.8 3.3 39 269-309 58-96 (438)
18 PRK00683 murD UDP-N-acetylmura 59.2 8.9 0.00019 38.4 3.2 31 276-308 59-89 (418)
19 TIGR03687 pupylate_cterm ubiqu 39.5 29 0.00063 24.3 2.3 23 115-137 4-26 (33)
20 PF13580 SIS_2: SIS domain; PD 32.5 63 0.0014 27.6 3.9 34 274-307 101-136 (138)
21 PRK13937 phosphoheptose isomer 28.9 2.1E+02 0.0045 25.7 6.8 37 273-309 103-141 (188)
22 cd05006 SIS_GmhA Phosphoheptos 26.6 2.7E+02 0.0059 24.4 7.0 39 272-310 97-137 (177)
23 cd05008 SIS_GlmS_GlmD_1 SIS (S 25.9 1.3E+02 0.0028 24.3 4.5 39 272-310 42-82 (126)
24 cd05014 SIS_Kpsf KpsF-like pro 23.8 1.6E+02 0.0034 23.9 4.6 44 267-310 38-83 (128)
25 PF02225 PA: PA domain; Inter 23.1 1.4E+02 0.003 23.2 4.0 34 275-309 32-65 (101)
26 PTZ00408 NAD-dependent deacety 22.1 3.6E+02 0.0078 25.8 7.3 63 274-339 170-235 (242)
27 cd04795 SIS SIS domain. SIS (S 22.0 1.8E+02 0.004 21.6 4.4 38 271-308 42-81 (87)
28 KOG2138 Predicted RNA binding 21.2 2E+02 0.0043 32.6 5.9 76 47-145 332-419 (883)
29 cd05710 SIS_1 A subgroup of th 20.9 2E+02 0.0043 23.8 4.7 39 271-309 42-82 (120)
30 PRK00230 orotidine 5'-phosphat 20.8 1.8E+02 0.0039 27.2 4.9 51 278-339 169-227 (230)
No 1
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=99.71 E-value=3.5e-17 Score=162.91 Aligned_cols=92 Identities=38% Similarity=0.484 Sum_probs=78.3
Q ss_pred cccccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhh
Q 043376 237 KFKMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEET 316 (348)
Q Consensus 237 ~m~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~ 316 (348)
|+.|.|.++++. +.|++|++|||+|++|+||||++|.++|||+||.+|+++||+++|+++....
T Consensus 1 ~~~~~~~~~~~~-------------~~i~~i~~DSR~v~~g~lFval~G~~~dGh~fi~~A~~~GA~~~v~~~~~~~--- 64 (460)
T PRK00139 1 MASMKLRDLLAP-------------VEITGLTYDSRKVKPGDLFVALPGHKVDGRDFIAQAIANGAAAVVAEADGEA--- 64 (460)
T ss_pred CccchHHHHhcC-------------CceeEEEeeccCcCCCCEEEEeCCCcCcHHHHHHHHHHCCCEEEEEcCcccc---
Confidence 355678887762 3578999999999999999999999999999999999999999999864210
Q ss_pred cCcceEEEeCCHHHHHHHHHHHHhhhhc
Q 043376 317 LGCKALVIVEDTNLVLPHWLPLFIGIRR 344 (348)
Q Consensus 317 ~~~ipvIvV~DtRkALg~LAAaFYg~Ps 344 (348)
...+|+|+|+|+++||+.||++||++|.
T Consensus 65 ~~~~~~i~V~d~~~al~~la~~~~~~~~ 92 (460)
T PRK00139 65 GTGVPVIIVPDLRKALALLAAAFYGHPS 92 (460)
T ss_pred CCCceEEEECCHHHHHHHHHHHHhcChh
Confidence 0135899999999999999999998884
No 2
>PRK14093 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional
Probab=99.67 E-value=2.3e-16 Score=158.29 Aligned_cols=100 Identities=23% Similarity=0.284 Sum_probs=80.8
Q ss_pred cccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcC
Q 043376 239 KMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLG 318 (348)
Q Consensus 239 ~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~ 318 (348)
.|++.+|++.+++. +.+.....|++|++|||+|++|+||||++|.++|||+||.+|+++||++||+++.... ....
T Consensus 6 ~~~~~~i~~~~~~~---~~~~~~~~i~~i~~DSR~v~~g~lFval~G~~~DGh~fi~~A~~~GA~~~v~~~~~~~-~~~~ 81 (479)
T PRK14093 6 LWTSDAMAEAMGAT---RSGALPRDVTGISIDSRTLAPGDAYFAIKGDVHDGHAFVAAALKAGAALAVVERAQRD-KFAA 81 (479)
T ss_pred ccCHHHHHHHhCCe---ecCCCCCceeEEEeecCCCCCCCEEEEeccCcCChHHHHHHHHHcCCcEEEEeccccc-ccCC
Confidence 47889998876542 2222245789999999999999999999999999999999999999999999863210 0002
Q ss_pred cceEEEeCCHHHHHHHHHHHHhhh
Q 043376 319 CKALVIVEDTNLVLPHWLPLFIGI 342 (348)
Q Consensus 319 ~ipvIvV~DtRkALg~LAAaFYg~ 342 (348)
.+|+|+|+|++++|+.||++||++
T Consensus 82 ~~~~i~V~d~~~al~~la~~~~~~ 105 (479)
T PRK14093 82 DAPLLVVDDVLAALRDLGRAARAR 105 (479)
T ss_pred CCCEEEECCHHHHHHHHHHHHHHh
Confidence 368999999999999999988865
No 3
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=99.67 E-value=2.5e-16 Score=156.74 Aligned_cols=96 Identities=26% Similarity=0.369 Sum_probs=81.1
Q ss_pred cccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcC
Q 043376 239 KMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLG 318 (348)
Q Consensus 239 ~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~ 318 (348)
.|++.+|++.+++. +.+ .+..|++|++|||+|+||+||||++|.++|||+||.+|+++||.+||+++... .
T Consensus 3 ~~~~~~l~~~~~~~---~~~-~~~~i~~v~~DSR~v~~g~lFval~G~~~dGh~fi~~A~~~Ga~~vv~~~~~~-----~ 73 (453)
T PRK10773 3 SVTLSQLADILNGE---LQG-ADITIDAVTTDTRKVTPGCLFVALKGERFDAHDFADDAKAAGAGALLVSRPLD-----I 73 (453)
T ss_pred CCCHHHHHHHhCCc---ccC-CCeeeeEEEeeCCCCCCCcEEEEecCCCCCHHHHHHHHHHCCCeEEEEecCcC-----C
Confidence 47899999876542 222 25679999999999999999999999999999999999999999999986421 1
Q ss_pred cceEEEeCCHHHHHHHHHHHHhhhh
Q 043376 319 CKALVIVEDTNLVLPHWLPLFIGIR 343 (348)
Q Consensus 319 ~ipvIvV~DtRkALg~LAAaFYg~P 343 (348)
..|+|+|+|++.+|+.||++||+++
T Consensus 74 ~~p~i~v~d~~~al~~la~~~~~~~ 98 (453)
T PRK10773 74 DLPQLVVKDTRLAFGQLAAWVRQQV 98 (453)
T ss_pred CCCEEEECCHHHHHHHHHHHHHhcC
Confidence 3579999999999999999887654
No 4
>PF01225 Mur_ligase: Mur ligase family, catalytic domain This Prosite entry is a subset of the Pfam family.; InterPro: IPR000713 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) [], MurD (6.3.2.9 from EC) [], MurE (6.3.2.13 from EC) [] and MurF (6.3.2.10 from EC) []. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the N-terminal domain of several stage 2 Mur ligases, including: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) []. The N-terminal domain is almost always associated with the cytoplasmic peptidoglycan synthetases C-terminal domain (see IPR004101 from INTERPRO).; GO: 0005524 ATP binding, 0009058 biosynthetic process; PDB: 2XJA_A 2WTZ_A 1E8C_A 3HN7_A 3EAG_A 1J6U_A 2AM2_A 2AM1_A 2F00_B 1GQY_B ....
Probab=99.66 E-value=2.5e-18 Score=134.00 Aligned_cols=78 Identities=37% Similarity=0.512 Sum_probs=66.1
Q ss_pred eeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccc----hhh-hcCcceEEEeCCHHHHHHHHHH
Q 043376 263 EITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEID----IEE-TLGCKALVIVEDTNLVLPHWLP 337 (348)
Q Consensus 263 eItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~----~~~-~~~~ipvIvV~DtRkALg~LAA 337 (348)
+|++|++|||+|++|+||||++|.++|||+||.+|+++||.++++++... ... .....++|.|+|++++|+.||+
T Consensus 1 ~i~~i~~dSr~v~~g~lF~a~~G~~~dG~~fi~~a~~~Ga~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~~~~~L~~la~ 80 (83)
T PF01225_consen 1 HIHGISIDSRKVSPGALFFAIKGERVDGHDFIEDAIAKGAAAVVVDKDASISPDNPEVPAADVPVIPVEDTRQALGELAA 80 (83)
T ss_dssp EEEEEETTSGGHHHHHHHHHHTTSEEEEECSCHHHHHTT-EEEESSSGGTSTTTSHHHHHHHHTTEEEEEHHHHHHHHHH
T ss_pred CEEEEEECcCccChhHEEEEcCCccccchhhhhHHHHCCCeEEEEcCccccccccHhHHhcCCCEEEECCHHHHHHHHHh
Confidence 47899999999999999999999999999999999999999999997651 000 0112468999999999999999
Q ss_pred HHh
Q 043376 338 LFI 340 (348)
Q Consensus 338 aFY 340 (348)
+||
T Consensus 81 ~~y 83 (83)
T PF01225_consen 81 AFY 83 (83)
T ss_dssp HHT
T ss_pred hhC
Confidence 987
No 5
>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetase. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown.
Probab=99.64 E-value=4.6e-16 Score=154.39 Aligned_cols=80 Identities=38% Similarity=0.590 Sum_probs=70.1
Q ss_pred ceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHHhh
Q 043376 262 VEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLFIG 341 (348)
Q Consensus 262 veItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaFYg 341 (348)
+.|++|++|||+|++|+||||++|.++|||+||.+|+++||++||+++.... ....+|+|+|+|+++||+.||++||+
T Consensus 2 ~~~~~v~~dsr~v~~g~lFval~G~~~dgh~fi~~A~~~GA~~~i~~~~~~~--~~~~~~~~~v~d~~~al~~la~~~~~ 79 (464)
T TIGR01085 2 LEVTGLTLDSREVKPGDLFVAIKGTHVDGHDFIHDAIANGAVAVVVERDVDF--YVAPVPVIIVPDLRHALSSLAAAFYG 79 (464)
T ss_pred CceeEEEecCcCCCCCCEEEEecCCcCCHHHHHHHHHHCCCeEEEEcccccc--ccCCceEEEECCHHHHHHHHHHHHhC
Confidence 4688999999999999999999999999999999999999999999974321 01135899999999999999998888
Q ss_pred hh
Q 043376 342 IR 343 (348)
Q Consensus 342 ~P 343 (348)
+|
T Consensus 80 ~~ 81 (464)
T TIGR01085 80 HP 81 (464)
T ss_pred Ch
Confidence 76
No 6
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=99.62 E-value=1.7e-15 Score=151.70 Aligned_cols=77 Identities=26% Similarity=0.286 Sum_probs=68.1
Q ss_pred cceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHHh
Q 043376 261 EVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLFI 340 (348)
Q Consensus 261 DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaFY 340 (348)
+..|++|++|||+|+||+||||+ |.++ ||+||++|+++||++||+++... ..+|+|+|+|+++||+.||++||
T Consensus 31 ~~~i~~i~~DSR~v~~g~lFva~-~~~~-gh~fi~~A~~~GA~~~v~~~~~~-----~~~~~i~V~d~~~al~~la~~~~ 103 (481)
T PRK14022 31 GVQFDDISYDSRTADEGTLFFAK-GAYF-KHKFLQNAITQGLKLYVSEKDYE-----VGIPQVIVPDIKKAMSLIAMEFY 103 (481)
T ss_pred CccEEEEEecCcCCCCCCEEEEc-CCCc-hHHHHHHHHHCCCeEEEEecccC-----CCCcEEEECCHHHHHHHHHHHHh
Confidence 55799999999999999999999 6677 99999999999999999986321 13579999999999999999999
Q ss_pred hhhc
Q 043376 341 GIRR 344 (348)
Q Consensus 341 g~Ps 344 (348)
++|+
T Consensus 104 ~~p~ 107 (481)
T PRK14022 104 DNPQ 107 (481)
T ss_pred cChh
Confidence 8874
No 7
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=99.61 E-value=2.8e-15 Score=159.30 Aligned_cols=101 Identities=25% Similarity=0.309 Sum_probs=80.3
Q ss_pred ccccHHHHHhhccCccccccCCCcceeeeeEeccCCC--CCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhh
Q 043376 238 FKMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVV--SAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEE 315 (348)
Q Consensus 238 m~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkV--kpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~ 315 (348)
|.|++.+|.+.++.. ..+..+..|++|++|||+| ++|+||||++|.++|||+||.+|+++||++||+++......
T Consensus 1 ~~~~~~~~~~~~~~~---~~~~~~~~i~~i~~DSR~v~~~~g~lFval~G~~~DGh~fi~~A~~~GA~~iv~~~~~~~~~ 77 (822)
T PRK11930 1 MSYTLESISGILGAE---GLGDKDAIIDQILTDSRSLSFPENTLFFALKGERNDGHRYIQELYEKGVRNFVVSEEKHPEE 77 (822)
T ss_pred CcccHHHHHHHhCCe---eccCCCceeCEEEecCCccCCCCCcEEEEeCCCCCCHHHHHHHHHHCCCEEEEEeccccccc
Confidence 467888888866532 1222256799999999999 99999999999999999999999999999999975311100
Q ss_pred hcCcceEEEeCCHHHHHHHHHHHHhh
Q 043376 316 TLGCKALVIVEDTNLVLPHWLPLFIG 341 (348)
Q Consensus 316 ~~~~ipvIvV~DtRkALg~LAAaFYg 341 (348)
....+|+|+|+|+++||+.||++||.
T Consensus 78 ~~~~~~~i~V~d~~~al~~la~~~~~ 103 (822)
T PRK11930 78 SYPDANFLKVKDPLKALQELAAYHRS 103 (822)
T ss_pred cCCCCCEEEECCHHHHHHHHHHHHHH
Confidence 01135899999999999999998875
No 8
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=99.59 E-value=3.4e-15 Score=160.39 Aligned_cols=101 Identities=29% Similarity=0.392 Sum_probs=78.2
Q ss_pred cccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcC
Q 043376 239 KMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLG 318 (348)
Q Consensus 239 ~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~ 318 (348)
++++.+++..+.++ .|. -..|++|++|||+|+||+||||++|.++|||+||.+|+++||++||+++.........
T Consensus 9 ~~~~~~~~~~~~~~----~~~-~~~~~~i~~DSR~v~~g~lFval~G~~~dGh~fi~~A~~~GA~~~v~~~~~~~~~~~~ 83 (958)
T PRK11929 9 NVKLEELLQALAWL----RGC-VAATADLRLDSREVQPGDLFVACRGAASDGRAFIDQALARGAAAVLVEAEGEDQVAAA 83 (958)
T ss_pred hhhHHHHHHHHHhh----ccc-ccccceeeeeccCCCCCCEEEEeCCCCCCHHHHHHHHHHcCCEEEEEeccccccccCC
Confidence 34555665544322 111 2358899999999999999999999999999999999999999999986421000001
Q ss_pred cceEEEeCCHHHHHHHHHHHHhhhhc
Q 043376 319 CKALVIVEDTNLVLPHWLPLFIGIRR 344 (348)
Q Consensus 319 ~ipvIvV~DtRkALg~LAAaFYg~Ps 344 (348)
.+|+|+|+|++++|+.||++||++|+
T Consensus 84 ~~~~i~V~d~~~al~~la~~~~~~p~ 109 (958)
T PRK11929 84 DALVLPVADLRKALGELAARWYGRPS 109 (958)
T ss_pred CCeEEEECCHHHHHHHHHHHHHhChh
Confidence 35899999999999999999999884
No 9
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ.
Probab=99.58 E-value=3.7e-15 Score=146.34 Aligned_cols=73 Identities=30% Similarity=0.395 Sum_probs=64.2
Q ss_pred eccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHHhhhhc
Q 043376 269 HDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLFIGIRR 344 (348)
Q Consensus 269 ~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaFYg~Ps 344 (348)
+|||+|+||+||||++|.++|||+||.+|+++||++||+++.... ...+|+|+|+|+++||+.||++||++|.
T Consensus 1 ~DSR~v~~g~lFval~G~~~dGh~fi~~A~~~Ga~~~i~~~~~~~---~~~~~~i~V~d~~~al~~la~~~~~~~~ 73 (417)
T TIGR01143 1 TDSRAIKPGDLFIALKGERFDGHDFVEQALAAGAVAVLVDREVGP---DNGLPQILVDDTLEALQALASAKRAKFS 73 (417)
T ss_pred CCCCccCCCcEEEEeCCCCCCHHHHHHHHHHCCCEEEEEcccccC---CCCCCEEEECCHHHHHHHHHHHHHhhCC
Confidence 599999999999999999999999999999999999999864210 1135799999999999999999998764
No 10
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=99.49 E-value=5.9e-14 Score=150.88 Aligned_cols=79 Identities=29% Similarity=0.360 Sum_probs=70.2
Q ss_pred cceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHHh
Q 043376 261 EVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLFI 340 (348)
Q Consensus 261 DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaFY 340 (348)
+..|++|++|||+|++|+||||++|.++|||+||.+|+++||++||+++.... ..+|+|+|+|++++|+.||.+||
T Consensus 523 ~~~i~~i~~dSr~v~~g~lFval~G~~~dGh~fi~~A~~~GA~~~i~~~~~~~----~~~~~i~V~d~~~al~~la~~~~ 598 (958)
T PRK11929 523 LPHAGAVSTDSRSVGRGELFVALRGENFDGHDYLPQAFAAGACAAVVERQVAD----VDLPQIVVDDTRAALGRLATAWR 598 (958)
T ss_pred CcccCeEEeeCCccCCCCEEEEecCCCCCHHHHHHHHHHcCCEEEEECCCccC----CCCCEEEeCCHHHHHHHHHHHHH
Confidence 56789999999999999999999999999999999999999999999864211 13579999999999999999888
Q ss_pred hhh
Q 043376 341 GIR 343 (348)
Q Consensus 341 g~P 343 (348)
+.+
T Consensus 599 ~~~ 601 (958)
T PRK11929 599 ARF 601 (958)
T ss_pred hcC
Confidence 765
No 11
>COG0770 MurF UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=99.46 E-value=1.6e-13 Score=139.08 Aligned_cols=99 Identities=29% Similarity=0.368 Sum_probs=79.6
Q ss_pred ccccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhc
Q 043376 238 FKMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETL 317 (348)
Q Consensus 238 m~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~ 317 (348)
|.|++.+++..+.+ .+.+.....+++|++|||+|.+|++|+|++|.++|||+|+.+|+++||.++++++.....
T Consensus 1 ~~~~~~~~~~~~~~---~~~~~~~~~~~~v~~Dsr~v~~g~lF~al~G~~~Dgh~fi~~A~~~GA~a~~v~r~~~~~--- 74 (451)
T COG0770 1 MLLTLDELADILGG---ALVGADPVVVSGVSIDSRKVKPGDLFVALKGERFDGHDFIEQALAAGAAAVLVARPVLPP--- 74 (451)
T ss_pred CcccHHHHHHHhCC---ccccCcccceeeEEeecccCCCCceeEEccCccccccchHHHHHhcCCEEEEEecCcCCc---
Confidence 45678888876643 233332256899999999999999999999999999999999999999999999864321
Q ss_pred Ccce--EEEeCCHHHHHHHHHHHHhhhhc
Q 043376 318 GCKA--LVIVEDTNLVLPHWLPLFIGIRR 344 (348)
Q Consensus 318 ~~ip--vIvV~DtRkALg~LAAaFYg~Ps 344 (348)
.++ ++.|.|+++||++||+ +|+..+
T Consensus 75 -~~~~~~~~V~d~~~al~~la~-~~~~~~ 101 (451)
T COG0770 75 -AIPLVVLLVLDTLEALGKLAK-AYRQKF 101 (451)
T ss_pred -ccccceEEeHHHHHHHHHHHH-HHHHhc
Confidence 224 8999999999999998 455443
No 12
>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=98.99 E-value=5.6e-10 Score=113.95 Aligned_cols=79 Identities=39% Similarity=0.534 Sum_probs=69.9
Q ss_pred eeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHHhhhhc
Q 043376 265 TGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLFIGIRR 344 (348)
Q Consensus 265 tgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaFYg~Ps 344 (348)
++++.|||+|++|+||+|++|.++|||.|+..|+++||+||+++...... ...+|+|+|++++.+++.+|..||+.|+
T Consensus 11 ~~l~~dsr~v~~g~lf~a~~g~~~~g~~~~~~a~~~Gavav~~~~~~~~~--~~~~~vi~V~~~~~~~~~~a~~~y~~ps 88 (475)
T COG0769 11 TGLTLDSRKVKEGDLFVAKPGTKVDGHDFIAGAIAPGAVAVVVEKDIKLA--EAGVPVIVVTGTNGKLTTLALAFYGLPS 88 (475)
T ss_pred ccceeehhhcCCCcEEEEEeccccccccchHhHhhCCCEEEEeccccccc--ccCCCEEEEcCcHHHHHHHHHHhccCcc
Confidence 78999999999999999999999999999999999999999999653111 1235689999999999999999999987
Q ss_pred c
Q 043376 345 R 345 (348)
Q Consensus 345 n 345 (348)
+
T Consensus 89 ~ 89 (475)
T COG0769 89 G 89 (475)
T ss_pred c
Confidence 3
No 13
>PF04613 LpxD: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD ; InterPro: IPR020573 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (2.3.1 from EC) catalyses an early step in lipid A biosynthesis []: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] = UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein] This enzyme contains several hexapeptide repeats and forms part of the wider bacterial transferase hexapeptide repeat family. This entry represents the non-repeating region of the enzyme.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0009245 lipid A biosynthetic process; PDB: 3PMO_A 3EH0_B 2IU9_A 2IU8_B 2IUA_A.
Probab=94.50 E-value=0.048 Score=42.17 Aligned_cols=70 Identities=33% Similarity=0.463 Sum_probs=42.2
Q ss_pred ceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHH
Q 043376 262 VEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLF 339 (348)
Q Consensus 262 veItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaF 339 (348)
+.|++|..= ...++|+|=|+ +..+|+..+....|.+||+.+..... .....++|+|+|++.++++++..|
T Consensus 3 ~~I~gva~l-~~A~~~~isF~------~~~ky~~~l~~s~A~avlv~~~~~~~-~~~~~~~iiv~nP~~afa~~~~~f 72 (72)
T PF04613_consen 3 IEISGVAPL-EEAGPGDISFL------DNPKYLKELKNSKAGAVLVPEEFAEE-VPEGKALIIVDNPRLAFAKLLQLF 72 (72)
T ss_dssp -EEEEEE-T-TT--TTEEEEE-------SSCGGGGGGG---SEEEEEHHHHTC-CCSSSEEEECS-HHHHHHHHHHHC
T ss_pred cEEeeecCh-hhcCCCCEEEe------cCHHHHHHHHhCCCeEEEEcchhccc-CCCCccEEEECCHHHHHHHHHHhC
Confidence 445555432 23678887555 23467888888889999998753221 123468999999999999999854
No 14
>COG1044 LpxD UDP-3-O-[3-hydroxymyristoyl]
Probab=92.62 E-value=0.32 Score=49.04 Aligned_cols=93 Identities=25% Similarity=0.233 Sum_probs=67.6
Q ss_pred ccccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhc
Q 043376 238 FKMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETL 317 (348)
Q Consensus 238 m~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~ 317 (348)
..++|.+|+..++. .+.+..++.|+++..= -+-.+++|+|. ++..|..+.....|.||+++...... ..
T Consensus 2 ~~~~l~~la~~~~~---e~~g~~~~~i~~va~l-~~a~~~~i~f~------~~~ky~~~l~~s~Agaviv~~~~~~~-~~ 70 (338)
T COG1044 2 PSYTLAELAQQLGA---ELRGDGDRVITGVAPL-DEAQPGDISFL------ANPKYRKELKTSRAGAVIVSAKDAAF-AP 70 (338)
T ss_pred ccchHHHHHHhhCc---EEecCCceeeeecchh-hhcCcccceee------cChhhhhhcccCcccEEEecHHHHhc-cc
Confidence 34689999987654 4566666777776543 34567887776 55689999999999999998753211 11
Q ss_pred CcceEEEeCCHHHHHHHHHHHHhh
Q 043376 318 GCKALVIVEDTNLVLPHWLPLFIG 341 (348)
Q Consensus 318 ~~ipvIvV~DtRkALg~LAAaFYg 341 (348)
...++++++++..+++.++..||.
T Consensus 71 ~~~~~Lv~~~P~~~fA~~~~~f~~ 94 (338)
T COG1044 71 AKKNALVVKDPYLAFAKVAQLFYR 94 (338)
T ss_pred CCceEEEeCCchHHHHHHHHHhcc
Confidence 234689999999999999998883
No 15
>PRK00892 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional
Probab=92.57 E-value=0.71 Score=45.32 Aligned_cols=95 Identities=23% Similarity=0.262 Sum_probs=63.4
Q ss_pred ccccHHHHHhhccCccccccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhc
Q 043376 238 FKMSLAELLDESKVVPVSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETL 317 (348)
Q Consensus 238 m~MtLsELLk~i~~~~~~l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~ 317 (348)
|+|+|++|++.++. .+.+..+.+|++++.=. ...+|+|=|. +...|+..+....|.++|+....... ..
T Consensus 1 ~~~~l~~i~~~~~~---~~~~~~~~~i~gva~l~-~a~~~~LsFl------~~~k~~~~l~~~~A~a~Iv~~d~~~~-~p 69 (343)
T PRK00892 1 MSLTLAELAELLGA---ELVGDGDIEITGVASLE-EAGPGQISFL------ANPKYRKQLATTKAGAVIVSPDDAEF-VP 69 (343)
T ss_pred CCccHHHHHHHhCC---EEeCCCCceEEeecccc-cCCCCeEEEE------cCchhHHHHhccCCeEEEechhhhhh-cc
Confidence 36899999997764 34555567787766433 3366786333 22467777767888888887653211 11
Q ss_pred CcceEEEeCCHHHHHHHHHHHHhhhh
Q 043376 318 GCKALVIVEDTNLVLPHWLPLFIGIR 343 (348)
Q Consensus 318 ~~ipvIvV~DtRkALg~LAAaFYg~P 343 (348)
....+|.+.|++.++..+...||..+
T Consensus 70 ~~~~~i~~~~p~~~~~~~~~~~~~~~ 95 (343)
T PRK00892 70 AGNALLVVKNPYLAFARLAQLFDPPA 95 (343)
T ss_pred CCceEEEeCCHHHHHHHHHHHhcccc
Confidence 23357899999999999998776443
No 16
>TIGR01853 lipid_A_lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase. This model describes LpxD, an enzyme for the biosynthesis of lipid A, a component oflipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species. This protein represents the third step from UDP-N-acetyl-D-glucosamine. The group added at this step generally is 14:0(3-OH) (myristate) but may vary; in Aquifex it appears to be 16:0(3-OH) (palmitate).
Probab=89.99 E-value=1.3 Score=43.65 Aligned_cols=78 Identities=22% Similarity=0.185 Sum_probs=55.1
Q ss_pred ccCCCcceeeeeEeccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHH
Q 043376 256 VYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHW 335 (348)
Q Consensus 256 l~G~~DveItgIS~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~L 335 (348)
+.++.+.+|++++.=- ...+|+|=|+. ..+|++.+....|.++|+.+..... ....++|+|+|++.+++++
T Consensus 10 ~~g~~~~~i~~~~~~~-~a~~~~l~f~~------~~k~~~~l~~~~a~aviv~~~~~~~--~~~~~~~~v~~p~~~~~~~ 80 (324)
T TIGR01853 10 LKGNGDIVITGVAPLE-KAKANHITFLA------NPKYLKHLKSSQAGAVIVSPDDQGL--PAKCAALVVKDPYLAFAKV 80 (324)
T ss_pred EeCCCCceEEcccChh-hCCCCeEEEEe------CHHHHHHHhhcCCcEEEecchhhcc--cCcceEEEECCHHHHHHHH
Confidence 3455567777765433 35788876662 3579999999999999997653211 1223688999999999999
Q ss_pred HHHHhhh
Q 043376 336 LPLFIGI 342 (348)
Q Consensus 336 AAaFYg~ 342 (348)
...||..
T Consensus 81 ~~~~~~~ 87 (324)
T TIGR01853 81 AELFDPP 87 (324)
T ss_pred HHHhccc
Confidence 9977544
No 17
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=62.02 E-value=7.7 Score=38.79 Aligned_cols=39 Identities=28% Similarity=0.297 Sum_probs=33.5
Q ss_pred eccCCCCCCCEEEEecccccchhhhHHHHHHcCCcEEEEcc
Q 043376 269 HDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASK 309 (348)
Q Consensus 269 ~DSRkVkpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe 309 (348)
.+++.+.++++||+-+|...| |.++.+|.++|+. |+.+.
T Consensus 58 ~~~~~~~~~d~vv~spgi~~~-~~~~~~a~~~g~~-v~~~~ 96 (438)
T PRK03806 58 LNDEWLLAADLIVASPGIALA-HPSLSAAADAGIE-IVGDI 96 (438)
T ss_pred CCHHHhcCCCEEEECCCCCCC-CHHHHHHHHCCCe-EEEHH
Confidence 356778889999999999988 9999999999998 66653
No 18
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=59.19 E-value=8.9 Score=38.40 Aligned_cols=31 Identities=29% Similarity=0.255 Sum_probs=26.4
Q ss_pred CCCEEEEecccccchhhhHHHHHHcCCcEEEEc
Q 043376 276 AGDLFVCCVGRKTDGHLYLSEADKRGAVAVVAS 308 (348)
Q Consensus 276 pGdLFVALkGer~DGHdFIeeAIeKGAvAVVvE 308 (348)
.-++||+.+|.+ ++|.|+.+|.++|+. |+.+
T Consensus 59 ~~dlvV~s~gi~-~~~~~l~~A~~~g~~-vv~~ 89 (418)
T PRK00683 59 QVDLVVRSPGIK-KEHPWVQAAIASHIP-VVTD 89 (418)
T ss_pred CCCEEEECCCCC-CCcHHHHHHHHCCCc-EEEH
Confidence 348999999999 889999999999986 4444
No 19
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=39.52 E-value=29 Score=24.35 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=20.3
Q ss_pred CCcchhHhHHHHHHhhHHHHHHh
Q 043376 115 EQDDFFGEIDKAVAMKRDEYVKK 137 (348)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~ 137 (348)
.-|++.+|||-.+..--++||+.
T Consensus 4 ~~D~lLDeId~vLe~NAe~FV~~ 26 (33)
T TIGR03687 4 GVDDLLDEIDGVLESNAEEFVRG 26 (33)
T ss_pred hHHHHHHHHHHHHHHhHHHHHHH
Confidence 45899999999999999999873
No 20
>PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D ....
Probab=32.52 E-value=63 Score=27.59 Aligned_cols=34 Identities=21% Similarity=0.352 Sum_probs=22.5
Q ss_pred CCCCCEEEEec--ccccchhhhHHHHHHcCCcEEEE
Q 043376 274 VSAGDLFVCCV--GRKTDGHLYLSEADKRGAVAVVA 307 (348)
Q Consensus 274 VkpGdLFVALk--Ger~DGHdFIeeAIeKGAvAVVv 307 (348)
++|||++|++. |.+..-...+..|-++|+..|..
T Consensus 101 ~~~gDvli~iS~SG~s~~vi~a~~~Ak~~G~~vIal 136 (138)
T PF13580_consen 101 IRPGDVLIVISNSGNSPNVIEAAEEAKERGMKVIAL 136 (138)
T ss_dssp --TT-EEEEEESSS-SHHHHHHHHHHHHTT-EEEEE
T ss_pred CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEE
Confidence 78999999996 55555556788888999988764
No 21
>PRK13937 phosphoheptose isomerase; Provisional
Probab=28.87 E-value=2.1e+02 Score=25.75 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=30.3
Q ss_pred CCCCCCEEEEe--cccccchhhhHHHHHHcCCcEEEEcc
Q 043376 273 VVSAGDLFVCC--VGRKTDGHLYLSEADKRGAVAVVASK 309 (348)
Q Consensus 273 kVkpGdLFVAL--kGer~DGHdFIeeAIeKGAvAVVvEe 309 (348)
.+.+|+++|++ .|.+.+=...++.|-++|+..|....
T Consensus 103 ~~~~~Dl~i~iS~sG~t~~~~~~~~~ak~~g~~~I~iT~ 141 (188)
T PRK13937 103 LGRPGDVLIGISTSGNSPNVLAALEKARELGMKTIGLTG 141 (188)
T ss_pred hCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEeC
Confidence 46899988888 47777777888999999999888765
No 22
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=26.65 E-value=2.7e+02 Score=24.36 Aligned_cols=39 Identities=18% Similarity=0.283 Sum_probs=32.4
Q ss_pred CCCCCCCEEEEe--cccccchhhhHHHHHHcCCcEEEEccc
Q 043376 272 RVVSAGDLFVCC--VGRKTDGHLYLSEADKRGAVAVVASKE 310 (348)
Q Consensus 272 RkVkpGdLFVAL--kGer~DGHdFIeeAIeKGAvAVVvEe~ 310 (348)
+.+.+|+++|++ .|.+.+-...+..|-++||..|.+...
T Consensus 97 ~~~~~~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~ 137 (177)
T cd05006 97 ALGQPGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGR 137 (177)
T ss_pred HhCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCC
Confidence 368899988887 488888888999999999999888643
No 23
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=25.93 E-value=1.3e+02 Score=24.34 Aligned_cols=39 Identities=21% Similarity=0.290 Sum_probs=31.0
Q ss_pred CCCCCCCEEEEe--cccccchhhhHHHHHHcCCcEEEEccc
Q 043376 272 RVVSAGDLFVCC--VGRKTDGHLYLSEADKRGAVAVVASKE 310 (348)
Q Consensus 272 RkVkpGdLFVAL--kGer~DGHdFIeeAIeKGAvAVVvEe~ 310 (348)
..+.+++++|++ .|...+--..++.|-++||..|.+...
T Consensus 42 ~~~~~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~ 82 (126)
T cd05008 42 PLLDEDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNV 82 (126)
T ss_pred CCCCCCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECC
Confidence 357899988777 587777778899999999998876543
No 24
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=23.76 E-value=1.6e+02 Score=23.89 Aligned_cols=44 Identities=20% Similarity=0.363 Sum_probs=33.8
Q ss_pred eEeccCCCCCCCEEEEe--cccccchhhhHHHHHHcCCcEEEEccc
Q 043376 267 IQHDSRVVSAGDLFVCC--VGRKTDGHLYLSEADKRGAVAVVASKE 310 (348)
Q Consensus 267 IS~DSRkVkpGdLFVAL--kGer~DGHdFIeeAIeKGAvAVVvEe~ 310 (348)
+......+.++++.|++ .|...+--.-++.|-++|+..|.....
T Consensus 38 ~~~~~~~~~~~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~ 83 (128)
T cd05014 38 LHGDLGMVTPGDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGN 83 (128)
T ss_pred hccccCcCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCC
Confidence 34456778899977776 577777778899999999998887653
No 25
>PF02225 PA: PA domain; InterPro: IPR003137 The PA (Protease associated) domain is found as an insert domain in diverse proteases, which include the MEROPS peptidase families A22B, M28, and S8A []. The PA domain is also found in a plant vacuolar sorting receptor O22925 from SWISSPROT and members of the RZF family, e.g. O43567 from SWISSPROT.; PDB: 3EIF_A 1XF1_B 3BXM_A 2C6P_A 1Z8L_C 3SJF_A 3BHX_A 2C6G_A 3D7F_A 2XEG_A ....
Probab=23.15 E-value=1.4e+02 Score=23.16 Aligned_cols=34 Identities=21% Similarity=0.209 Sum_probs=24.4
Q ss_pred CCCCEEEEecccccchhhhHHHHHHcCCcEEEEcc
Q 043376 275 SAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASK 309 (348)
Q Consensus 275 kpGdLFVALkGer~DGHdFIeeAIeKGAvAVVvEe 309 (348)
-.|.+-+|.+|.-.- .+=+..|.++||.+||+=.
T Consensus 32 ~~gkIvlv~rg~~~~-~~k~~~a~~~GA~gvIi~~ 65 (101)
T PF02225_consen 32 VKGKIVLVERGSCSF-DDKVRNAQKAGAKGVIIYN 65 (101)
T ss_dssp CTTSEEEEESTSSCH-HHHHHHHHHTTESEEEEE-
T ss_pred ccceEEEEecCCCCH-HHHHHHHHHcCCEEEEEEe
Confidence 478888888887532 3446778899999988755
No 26
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=22.08 E-value=3.6e+02 Score=25.79 Aligned_cols=63 Identities=21% Similarity=0.288 Sum_probs=43.6
Q ss_pred CCCCCEEEEecccc---cchhhhHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHH
Q 043376 274 VSAGDLFVCCVGRK---TDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLF 339 (348)
Q Consensus 274 VkpGdLFVALkGer---~DGHdFIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaF 339 (348)
+..-+||+++ |+. .-...++..|.++|+..|++........ .....++.-+..++|..|++.+
T Consensus 170 ~~~~Dlllvi-GTSl~V~pa~~l~~~a~~~g~~vi~IN~~~~~~~--~~~~~~i~g~~~~~l~~l~~~~ 235 (242)
T PTZ00408 170 MSKTDLFVAV-GTSGNVYPAAGFVGRAQFYGATTLELNLEEGTNY--SQFDESIYGKASVIVPAWVDRV 235 (242)
T ss_pred HHhCCEEEEE-ccCCccccHHHHHHHHHHcCCeEEEECCCCCCCC--ccCCEEEECCHHHHHHHHHHHH
Confidence 6677888885 665 6677889999999999999886432111 1112344567888888887654
No 27
>cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=21.98 E-value=1.8e+02 Score=21.60 Aligned_cols=38 Identities=18% Similarity=0.271 Sum_probs=28.4
Q ss_pred cCCCCCCCEEEEe--cccccchhhhHHHHHHcCCcEEEEc
Q 043376 271 SRVVSAGDLFVCC--VGRKTDGHLYLSEADKRGAVAVVAS 308 (348)
Q Consensus 271 SRkVkpGdLFVAL--kGer~DGHdFIeeAIeKGAvAVVvE 308 (348)
.+.+.+++++|++ .|...+=-.-++.|-++|+..|...
T Consensus 42 ~~~~~~~d~~i~iS~sg~t~~~~~~~~~a~~~g~~ii~it 81 (87)
T cd04795 42 LSLLRKGDVVIALSYSGRTEELLAALEIAKELGIPVIAIT 81 (87)
T ss_pred HhcCCCCCEEEEEECCCCCHHHHHHHHHHHHcCCeEEEEe
Confidence 5677899977776 5766666677888888998877653
No 28
>KOG2138 consensus Predicted RNA binding protein, contains G-patch domain [RNA processing and modification]
Probab=21.23 E-value=2e+02 Score=32.58 Aligned_cols=76 Identities=18% Similarity=0.319 Sum_probs=47.9
Q ss_pred CCCCCCCCCC------CCCCCccccccchhHHHHHH------HHHHHHHhhHHHhhhccchhhhhcccCCCCCCCCCCCC
Q 043376 47 KFYPTPSDDD------PPEAPEDTAHGVSKFQQIHR------QAAKARKRQEDDFKANQSTYLNAIADVDDPPVNTGDVS 114 (348)
Q Consensus 47 ~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (348)
.-||.|.|.. ----++++.||.+-..+.+| |- .+++--||++|++.
T Consensus 332 ~~rp~Pmd~~~~~~s~~~kly~~~~~~khqlNa~qra~~lGe~~-q~~~t~eeq~kr~~--------------------- 389 (883)
T KOG2138|consen 332 RHRPAPMDKERAQKSETAKLYKRSGLGKHQLNADQRAQILGEQQ-QEEKTAEEQPKRNP--------------------- 389 (883)
T ss_pred ccCCCcchhhHhhhhhhcccccccccchhhcCHHHHHHhhccch-hhhhhhhhhhhccc---------------------
Confidence 5567777765 22346788888887777777 33 67777788888763
Q ss_pred CCcchhHhHHHHHHhhHHHHHHhccCCCCCC
Q 043376 115 EQDDFFGEIDKAVAMKRDEYVKKGLIKPKKR 145 (348)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (348)
+-|+--++=-++..+-..+..+|++.-+++
T Consensus 390 -~k~~~k~~k~~~~~r~~~le~rg~~~~~~~ 419 (883)
T KOG2138|consen 390 -FKDHSKSMKQATDLRAAQLEARGLAQNAQS 419 (883)
T ss_pred -hHhhhHHHHhhhhHHHHHHhhccccccCch
Confidence 234444455555566666667776655533
No 29
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=20.89 E-value=2e+02 Score=23.83 Aligned_cols=39 Identities=10% Similarity=0.187 Sum_probs=31.5
Q ss_pred cCCCCCCCEEEEec--ccccchhhhHHHHHHcCCcEEEEcc
Q 043376 271 SRVVSAGDLFVCCV--GRKTDGHLYLSEADKRGAVAVVASK 309 (348)
Q Consensus 271 SRkVkpGdLFVALk--Ger~DGHdFIeeAIeKGAvAVVvEe 309 (348)
...+.+++++|++. |...+--+-++.|-++|+..|.+..
T Consensus 42 ~~~~~~~dl~I~iS~SG~t~~~~~~~~~a~~~g~~vi~iT~ 82 (120)
T cd05710 42 PKRLTEKSVVILASHSGNTKETVAAAKFAKEKGATVIGLTD 82 (120)
T ss_pred cccCCCCcEEEEEeCCCCChHHHHHHHHHHHcCCeEEEEEC
Confidence 45788999888874 8877877888899999999887764
No 30
>PRK00230 orotidine 5'-phosphate decarboxylase; Reviewed
Probab=20.84 E-value=1.8e+02 Score=27.24 Aligned_cols=51 Identities=16% Similarity=0.192 Sum_probs=34.3
Q ss_pred CEEEEecccccchhh--------hHHHHHHcCCcEEEEccccchhhhcCcceEEEeCCHHHHHHHHHHHH
Q 043376 278 DLFVCCVGRKTDGHL--------YLSEADKRGAVAVVASKEIDIEETLGCKALVIVEDTNLVLPHWLPLF 339 (348)
Q Consensus 278 dLFVALkGer~DGHd--------FIeeAIeKGAvAVVvEe~~~~~~~~~~ipvIvV~DtRkALg~LAAaF 339 (348)
.+..-.+|.+..|-. -+.+|++.||..||+-+. +..-+|+.+++..+....
T Consensus 169 ~~~~v~pGI~~~g~~~~dq~~~~~~~~ai~~Gad~iVvGR~-----------I~~a~dP~~~a~~i~~~i 227 (230)
T PRK00230 169 DFLLVTPGIRPAGSDAGDQKRVMTPAQAIAAGSDYIVVGRP-----------ITQAADPAAAYEAILAEI 227 (230)
T ss_pred ceEEEcCCcCCCCCCcchHHHHhCHHHHHHcCCCEEEECCc-----------ccCCCCHHHHHHHHHHHh
Confidence 333333676654422 588999999999998753 344568888887776643
Done!