Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_057507018.1 ABB28_RS02085 propionate--CoA ligase
Query= BRENDA::P77495 (628 letters) >NCBI__GCF_001431535.1:WP_057507018.1 Length = 626 Score = 760 bits (1963), Expect = 0.0 Identities = 366/627 (58%), Positives = 472/627 (75%), Gaps = 4/627 (0%) Query: 1 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60 M + E Y+RSI+EPE FW E+A RI W P Q LD+SNPPF RW+ G TNLC+NA+DR Sbjct: 1 MDYEETYRRSIDEPEAFWGEEANRIYWHKPPRQVLDYSNPPFRRWYVGGETNLCYNAVDR 60 Query: 61 WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120 L ++P+ LAL+AVS+ET R T+RQL+ EVN A++L+ L V GDRV++YMP +AE Sbjct: 61 HLAERPDQLALVAVSTETGTTREITYRQLYREVNDFAAVLKRLDVGHGDRVVIYMPNMAE 120 Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180 A +LACARIGA+HSVVFGGFA+H++A RIDDA+P L+++ADAG RGGK+IPYK ++D Sbjct: 121 AVFAMLACARIGAVHSVVFGGFAAHNLALRIDDARPKLLIAADAGMRGGKLIPYKGMVDA 180 Query: 181 AISQAQHQPRHVLLVDRGLAKMA-RVSGRDVDFASLRHQHIGARVPVAWLESNETSCILY 239 A ++AQ+ P HVL+V RGL R +GRDVD+A+LR + VPV WLES+E S +LY Sbjct: 181 ACAEAQNPPPHVLIVSRGLDPAEPRQAGRDVDYATLRAEVGEVDVPVQWLESSEPSYLLY 240 Query: 240 TSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLA 299 TSGTTGKPKGVQRDVGGYAVA+A SM T+F + G V F SD+GW VGHSY VY PL+ Sbjct: 241 TSGTTGKPKGVQRDVGGYAVAMAQSMQTVFDCQPGQVMFSTSDVGWAVGHSYNVYGPLIG 300 Query: 300 GMATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVL 359 G +++YEGLPT PD G+WW + E+Y V +FS+PTAIRVLKK IR+HDL +L+ + Sbjct: 301 GCTSLLYEGLPTNPDPGIWWALCEQYNVRTLFSSPTAIRVLKKHDVDFIRRHDLKALKYI 360 Query: 360 YLAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGY 419 +LAGEPLDEPTA W + L P+IDNYWQTE+GWP + + GLD +P R GSPG P GY Sbjct: 361 FLAGEPLDEPTAHWANEALGKPIIDNYWQTETGWPALTLLPGLDMKPVRFGSPGFPNLGY 420 Query: 420 NVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDW 479 +++++E TG +KG+LV+ PLPPGC+ T+W DD RF+++Y+S F +Y++ DW Sbjct: 421 RMKVIDENTGVEVAPGQKGVLVMTPPLPPGCMSTVWNDDARFLQSYFSHFKELLYSSLDW 480 Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539 IRD DGY FILGRTDDVINVAGHRLGTREIEE+IS HP VAE AV+GVKD LKGQV + Sbjct: 481 AIRDEDGYTFILGRTDDVINVAGHRLGTREIEEAISGHPRVAEAAVIGVKDELKGQVPLV 540 Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599 FV K+ + ED ++ +MA V + +G RPAH+ V+ LPKTRSGK+LRR++Q Sbjct: 541 FVTLKQGLNGEDPAPVVAE---MMAAVTASLGAVARPAHIHVVNALPKTRSGKLLRRSLQ 597 Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAM 626 A+ E RDPGDL+T+DDPA+LD+IR+A+ Sbjct: 598 ALAEQRDPGDLSTLDDPAALDEIRRAL 624 Lambda K H 0.320 0.136 0.422 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1216 Number of extensions: 43 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 628 Length of database: 626 Length adjustment: 38 Effective length of query: 590 Effective length of database: 588 Effective search space: 346920 Effective search space used: 346920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 bits)
Align candidate WP_057507018.1 ABB28_RS02085 (propionate--CoA ligase)
to HMM TIGR02316 (prpE: propionate--CoA ligase (EC 6.2.1.17))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR02316.hmm # target sequence database: /tmp/gapView.9054.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02316 [M=628] Accession: TIGR02316 Description: propion_prpE: propionate--CoA ligase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1114.1 0.0 0 1113.9 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057507018.1 ABB28_RS02085 propionate--CoA li Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507018.1 ABB28_RS02085 propionate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1113.9 0.0 0 0 1 627 [. 1 625 [. 1 626 [] 0.98 Alignments for each domain: == domain 1 score: 1113.9 bits; conditional E-value: 0 TIGR02316 1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeql 69 m yee y+rsi+epeafw+e+a+ri w+ p+ +vld+sn+pf+rw+vgg+tnlcynavdrhl++r++ql lcl|NCBI__GCF_001431535.1:WP_057507018.1 1 MDYEETYRRSIDEPEAFWGEEANRIYWHKPPRQVLDYSNPPFRRWYVGGETNLCYNAVDRHLAERPDQL 69 68******************************************************************* PP TIGR02316 70 alvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvv 138 alvavs+etg++r++tyrql+revn +a++l+ l v+ gdrv+iy+p++aea++a+lacariga+hsvv lcl|NCBI__GCF_001431535.1:WP_057507018.1 70 ALVAVSTETGTTREITYRQLYREVNDFAAVLKRLDVGHGDRVVIYMPNMAEAVFAMLACARIGAVHSVV 138 ********************************************************************* PP TIGR02316 139 fggfashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglak.lrrvp 206 fggfa+h+la+ridda+pkl+++adag+rggk+i+yk ++daa+aeaq++p+hvl+v+rgl++ r + lcl|NCBI__GCF_001431535.1:WP_057507018.1 139 FGGFAAHNLALRIDDARPKLLIAADAGMRGGKLIPYKGMVDAACAEAQNPPPHVLIVSRGLDPaEPRQA 207 ***************************************************************556889 PP TIGR02316 207 grdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagd 275 grdvdya+lr + + dv+v+wles+epsy+lytsgttgkpkgvqrdvggyava+a sm+++f+ + g+ lcl|NCBI__GCF_001431535.1:WP_057507018.1 208 GRDVDYATLRAEVGEVDVPVQWLESSEPSYLLYTSGTTGKPKGVQRDVGGYAVAMAQSMQTVFDCQPGQ 276 ********************************************************************* PP TIGR02316 276 vlfsasdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqd 344 v+fs+sdvgw+vghsy+vy+pl+ g +++lyeglpt+pd+g+ww+++e+y+v+++fs+ptairvlkk+d lcl|NCBI__GCF_001431535.1:WP_057507018.1 277 VMFSTSDVGWAVGHSYNVYGPLIGGCTSLLYEGLPTNPDPGIWWALCEQYNVRTLFSSPTAIRVLKKHD 345 ********************************************************************* PP TIGR02316 345 aallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspg 413 +r+hdl +l+++flagepldepta+w ++algkp+idnywqtetgwp l++ +gld kpv++gspg lcl|NCBI__GCF_001431535.1:WP_057507018.1 346 VDFIRRHDLKALKYIFLAGEPLDEPTAHWANEALGKPIIDNYWQTETGWPALTLLPGLDMKPVRFGSPG 414 ********************************************************************* PP TIGR02316 414 lpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafkrllyssldwgir 482 +p gyr++v+de tg +v+p++kg+lv+++plppgc+stvw+ddarfl++yfs+fk+llyssldw+ir lcl|NCBI__GCF_001431535.1:WP_057507018.1 415 FPNLGYRMKVIDENTGVEVAPGQKGVLVMTPPLPPGCMSTVWNDDARFLQSYFSHFKELLYSSLDWAIR 483 ********************************************************************* PP TIGR02316 483 dedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsved 551 dedgytfilgrtddvinvaghrlgtreiee++s h+ vae+av+gvkdelkgqv+++f++lk+ + e lcl|NCBI__GCF_001431535.1:WP_057507018.1 484 DEDGYTFILGRTDDVINVAGHRLGTREIEEAISGHPRVAEAAVIGVKDELKGQVPLVFVTLKQGLNGE- 551 **************************************************************665544. PP TIGR02316 552 addahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaale 620 d+ + +e+ma+v + lgavarpa+++vv+alpktrsgkllrr++qa+ae rdpgdl+t+ddpaal+ lcl|NCBI__GCF_001431535.1:WP_057507018.1 552 --DPAPVVAEMMAAVTASLGAVARPAHIHVVNALPKTRSGKLLRRSLQALAEQRDPGDLSTLDDPAALD 618 ..55667789*********************************************************** PP TIGR02316 621 qvreale 627 ++r+al lcl|NCBI__GCF_001431535.1:WP_057507018.1 619 EIRRALG 625 *****85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (628 nodes) Target sequences: 1 (626 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 11.39 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory