Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011766904.1 AZO_RS15950 propionate--CoA ligase
Query= BRENDA::P77495 (628 letters) >NCBI__GCF_000061505.1:WP_011766904.1 Length = 630 Score = 792 bits (2045), Expect = 0.0 Identities = 380/627 (60%), Positives = 484/627 (77%), Gaps = 3/627 (0%) Query: 2 SFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRW 61 ++ EF++RSI++ ++FWAEQA+ +DW P Q D S PPF +WF G TNLC+NA+DR Sbjct: 3 NYKEFHRRSIDQRDEFWAEQAQLVDWHKPAEQICDFSKPPFVKWFKGGETNLCYNAVDRH 62 Query: 62 LEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEA 121 K+P+ AL+ +S+ET EE+ ++F +L EV +A++ + LGV+RGDRVL+YMPMIAEA Sbjct: 63 AAKRPDDRALVYISTETNEEKVYSFAELQREVERMAAIYQDLGVKRGDRVLIYMPMIAEA 122 Query: 122 HITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDA 181 +LACARIGAIHSVVFGGFA+ S+A RIDDAKPVL+VS+DAG R GK +PYK L+D+A Sbjct: 123 AFAMLACARIGAIHSVVFGGFAAGSLATRIDDAKPVLMVSSDAGMRNGKPVPYKHLVDEA 182 Query: 182 ISQAQHQPRHVLLVDRGLAK-MARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240 A+ P VL+VDRGL K +V RDVD+A LR +HI A+VPV WLES+E S ILYT Sbjct: 183 CKLAEFPPAKVLIVDRGLDKGFPKVESRDVDYAELRAKHIDAKVPVTWLESSEPSYILYT 242 Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300 SGTTGKPKGVQRD GGY VALA SM IF G +G F SDIGWVVGHSYI+Y PL+AG Sbjct: 243 SGTTGKPKGVQRDTGGYTVALAASMKHIFTGGSGETMFSTSDIGWVVGHSYIIYGPLIAG 302 Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360 MATI+YEG P PD G+WW IVEKY+VS MFSAPTA+RVLKK A ++K+DLSSL+ L+ Sbjct: 303 MATIMYEGTPLRPDAGIWWQIVEKYKVSVMFSAPTAVRVLKKQDPAFLKKYDLSSLKHLF 362 Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420 LAGEPLDE + W+ + L +PVIDNYWQTE+GWP++AI RG++D +LGSP P+YGY+ Sbjct: 363 LAGEPLDETSHKWIMSELGIPVIDNYWQTETGWPMLAIVRGVEDSKIKLGSPAFPVYGYD 422 Query: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRP-VYATFDW 479 +++ E G CG NEKG++ + PLPPGC+ T+WG D RFV TY+SLF+ P VY++ DW Sbjct: 423 LRIFRE-DGSECGPNEKGIVGIVPPLPPGCLSTVWGQDERFVSTYFSLFTDPVVYSSSDW 481 Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539 GI+D +GYH ILGR DDVINVAGHRLGTREIEE++ +HP +AEVAVVGV D LKGQ+ +A Sbjct: 482 GIKDENGYHTILGRMDDVINVAGHRLGTREIEEAVQTHPAIAEVAVVGVHDELKGQMPMA 541 Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599 F + K++ +++ + + EK +M VD +G RPA V F++ LPKTRSGKMLRR+IQ Sbjct: 542 FAVVKDASTVDTAEKRAALEKEVMKKVDESLGAIARPARVHFINGLPKTRSGKMLRRSIQ 601 Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAM 626 A+ EGRD GDLTTIDDP +LDQI+ A+ Sbjct: 602 ALAEGRDAGDLTTIDDPTTLDQIKAAL 628 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: 1206 Number of extensions: 41 Number of successful extensions: 4 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: 630 Length adjustment: 38 Effective length of query: 590 Effective length of database: 592 Effective search space: 349280 Effective search space used: 349280 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_011766904.1 AZO_RS15950 (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.3517763.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 1078.5 0.1 0 1078.2 0.1 1.0 1 NCBI__GCF_000061505.1:WP_011766904.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000061505.1:WP_011766904.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1078.2 0.1 0 0 2 626 .. 3 628 .. 2 630 .] 0.99 Alignments for each domain: == domain 1 score: 1078.2 bits; conditional E-value: 0 TIGR02316 2 ayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalvav 74 +y+e+++rsi++ ++fwaeqa+ +dw+ p +++ d s++pf +wf gg+tnlcynavdrh +kr+++ alv++ NCBI__GCF_000061505.1:WP_011766904.1 3 NYKEFHRRSIDQRDEFWAEQAQLVDWHKPAEQICDFSKPPFVKWFKGGETNLCYNAVDRHAAKRPDDRALVYI 75 69*********************************************************************** PP TIGR02316 75 ssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashsl 147 s+et+ee+ +++ +l rev+++a++ + lgv+rgdrvliy+pmiaeaa+a+lacarigaihsvvfggfa+ sl NCBI__GCF_000061505.1:WP_011766904.1 76 STETNEEKVYSFAELQREVERMAAIYQDLGVKRGDRVLIYMPMIAEAAFAMLACARIGAIHSVVFGGFAAGSL 148 ************************************************************************* PP TIGR02316 148 aariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglak.lrrvpgrdvdyaalrrqh 219 a+ridda+p+l+vs+dag+r gk ++yk+l+d+a++ a +pa+vl+vdrgl+k + +v +rdvdya lr +h NCBI__GCF_000061505.1:WP_011766904.1 149 ATRIDDAKPVLMVSSDAGMRNGKPVPYKHLVDEACKLAEFPPAKVLIVDRGLDKgFPKVESRDVDYAELRAKH 221 ******************************************************99***************** PP TIGR02316 220 edadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyi 292 +da+v+v wles+epsyilytsgttgkpkgvqrd+ggy+valaasm+ if + +g+++fs+sd+gwvvghsyi NCBI__GCF_000061505.1:WP_011766904.1 222 IDAKVPVTWLESSEPSYILYTSGTTGKPKGVQRDTGGYTVALAASMKHIFTGGSGETMFSTSDIGWVVGHSYI 294 ************************************************************************* PP TIGR02316 293 vyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagep 365 +y+pl+ag+at++yeg+p rpd+g+ww+iveky+vsvmfsapta+rvlkkqd+a l+k+dlssl++lflagep NCBI__GCF_000061505.1:WP_011766904.1 295 IYGPLIAGMATIMYEGTPLRPDAGIWWQIVEKYKVSVMFSAPTAVRVLKKQDPAFLKKYDLSSLKHLFLAGEP 367 ************************************************************************* PP TIGR02316 366 ldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvygyrldvldeatgedvgpnekg 438 lde + +wi lg pvidnywqtetgwp+lai+rg++d+ klgsp +pvygy+l+++ e g ++gpnekg NCBI__GCF_000061505.1:WP_011766904.1 368 LDETSHKWIMSELGIPVIDNYWQTETGWPMLAIVRGVEDSKIKLGSPAFPVYGYDLRIFRE-DGSECGPNEKG 439 ***********************************************************99.699******** PP TIGR02316 439 llvvaaplppgclstvwgddarflktyfsafkrl.lyssldwgirdedgytfilgrtddvinvaghrlgtrei 510 ++ +++plppgclstvwg+d rf+ tyfs+f+++ +yss dwgi+de+gy++ilgr ddvinvaghrlgtrei NCBI__GCF_000061505.1:WP_011766904.1 440 IVGIVPPLPPGCLSTVWGQDERFVSTYFSLFTDPvVYSSSDWGIKDENGYHTILGRMDDVINVAGHRLGTREI 512 ********************************6527************************************* PP TIGR02316 511 eesvsshaavaevavvgvkdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarparvyvva 583 ee+v +h+a+aevavvgv+delkgq+++afa++k+a++v+ a+++ aleke+m+ v++ lga+arparv++++ NCBI__GCF_000061505.1:WP_011766904.1 513 EEAVQTHPAIAEVAVVGVHDELKGQMPMAFAVVKDASTVDTAEKRAALEKEVMKKVDESLGAIARPARVHFIN 585 ************************************************************************* PP TIGR02316 584 alpktrsgkllrraiqavaegrdpgdlttiddpaaleqvreal 626 lpktrsgk+lrr+iqa+aegrd gdlttiddp++l+q++ al NCBI__GCF_000061505.1:WP_011766904.1 586 GLPKTRSGKMLRRSIQALAEGRDAGDLTTIDDPTTLDQIKAAL 628 ****************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (628 nodes) Target sequences: 1 (630 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 32.74 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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