Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate WP_057509261.1 ABB28_RS14270 malate synthase A
Query= ecocyc::MALATE-SYNTHASE (533 letters) >NCBI__GCF_001431535.1:WP_057509261.1 Length = 545 Score = 501 bits (1290), Expect = e-146 Identities = 267/520 (51%), Positives = 338/520 (65%), Gaps = 17/520 (3%) Query: 21 EKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGTLPDFISETASIRDADWKI 80 + +L A + L L P R LAAR+Q+Q D G LPDF ++TA IR DWK+ Sbjct: 28 QSALLPAPLLALLVSLHRAVEPGRQARLAARVQRQAFFDQGGLPDFRTDTAPIRAEDWKV 87 Query: 81 RGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPDWNKVIDGQINLRDAV 140 +PA L DRRVEITGP + KMVINALN+ KVFMADFED+ AP W ++ GQ +L AV Sbjct: 88 APLPAALLDRRVEITGPTDPKMVINALNSGAKVFMADFEDATAPTWGNLLAGQQSLIGAV 147 Query: 141 NGTISYTNEAG-----KIYQLKP--NPAVLICRVRGLHLPEKHVTWRGEAIPGSLFDFAL 193 G + +T A K Y L+P AVLI R RG HL EKHV G+ + G LFD A+ Sbjct: 148 RGDLQFTAPASGSKPSKHYSLRPYEERAVLIVRPRGWHLDEKHVLVDGQRLAGGLFDAAV 207 Query: 194 YFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLP 253 + +HN + L+A GPYFYLPK QS +EAA W S+ E LP G IK T+LIETLP Sbjct: 208 FAYHNARTLMANDRGPYFYLPKLQSMEEAALWETALSHIEGMLGLPHGQIKVTVLIETLP 267 Query: 254 AVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSR 313 AVF+MDEILHALRD IVGLNCGRWDYIFSY+KT + + D+VLP+R VTM +PFL AYS Sbjct: 268 AVFEMDEILHALRDRIVGLNCGRWDYIFSYLKTFRRHADKVLPERGQVTMTQPFLKAYSE 327 Query: 314 LLIKTCHKRGAFAMGGMAAFIP-SKDEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLA 372 LLI+TCH+RGA AMGGMAA IP D N Q + +V+ADK E GHDGTW+AHP L Sbjct: 328 LLIQTCHRRGAHAMGGMAAQIPIGNDAAANEQAMARVRADKLREVTAGHDGTWVAHPALI 387 Query: 373 DTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRANIRVAVQYIEAW 432 AMA+F++ + NQ +V+R QD + DQL+A G + G N+ V V+Y+ AW Sbjct: 388 PVAMAIFDEHMPG-ANQQQVLR-QDVRVDRDQLIARPPGSISRAGFEGNVEVCVRYLAAW 445 Query: 433 ISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQ-KTLSNGKPVTKALFRQMLGEEMKVIA 491 + GNGCVPI+ LMEDAATAEISR+ +WQW+H + L +G + AL L + + Sbjct: 446 LDGNGCVPIHNLMEDAATAEISRSQLWQWLHTPGQQLDDGTAIDAALLDNALAQ----LP 501 Query: 492 SELGEERF--SQGRFDDAARLMEQITTSDELIDFLTLPGY 529 + LG+ GR D+A L+ +++ +DEL DFLTLP Y Sbjct: 502 ARLGDRATLPGGGRVDEAIALLAELSRADELNDFLTLPAY 541 Lambda K H 0.320 0.135 0.407 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: 776 Number of extensions: 34 Number of successful extensions: 5 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: 533 Length of database: 545 Length adjustment: 35 Effective length of query: 498 Effective length of database: 510 Effective search space: 253980 Effective search space used: 253980 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: 52 (24.6 bits)
Align candidate WP_057509261.1 ABB28_RS14270 (malate synthase A)
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))
# 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.carbon/TIGR01344.hmm # target sequence database: /tmp/gapView.27592.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01344 [M=511] Accession: TIGR01344 Description: malate_syn_A: malate synthase A 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-211 687.5 0.0 4.9e-211 687.3 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509261.1 ABB28_RS14270 malate synthase A Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509261.1 ABB28_RS14270 malate synthase A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 687.3 0.0 4.9e-211 4.9e-211 5 510 .. 35 544 .. 31 545 .] 0.97 Alignments for each domain: == domain 1 score: 687.3 bits; conditional E-value: 4.9e-211 TIGR01344 5 ealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitG 73 l++l++lhr ++ r++ la+r ++qa +d+g l+df +t+ ir++dwkva++pa+lldrrveitG lcl|NCBI__GCF_001431535.1:WP_057509261.1 35 PLLALLVSLHRAVEPGRQARLAARVQRQAFFDQGGLPDFRTDTAPIRAEDWKVAPLPAALLDRRVEITG 103 568899*************************************************************** PP TIGR01344 74 PvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesg....keyalk..a 136 P+d kmvinaln++akvf+adfed+++Ptw n++ Gq +l a+rg+++ft++ sg k+y l+ lcl|NCBI__GCF_001431535.1:WP_057509261.1 104 PTDPKMVINALNSGAKVFMADFEDATAPTWGNLLAGQQSLIGAVRGDLQFTAPASGskpsKHYSLRpyE 172 ***************************************************9765433339*****777 PP TIGR01344 137 klavlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwnd 205 ++avlivrprGwhl e+h+ +dg+ ++g l+d +++++hnar+l+++ +GPyfylPkl+s ea lw+ lcl|NCBI__GCF_001431535.1:WP_057509261.1 173 ERAVLIVRPRGWHLDEKHVLVDGQRLAGGLFDAAVFAYHNARTLMANDRGPYFYLPKLQSMEEAALWET 241 99******************************************************************* PP TIGR01344 206 vfllaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlP 274 + + +lglp+G ik tvlietlpa+femdeil+ lr+ ++GlncGrwdyifs++k+++++ ++vlP lcl|NCBI__GCF_001431535.1:WP_057509261.1 242 ALSHIEGMLGLPHGQIKVTVLIETLPAVFEMDEILHALRDRIVGLNCGRWDYIFSYLKTFRRHADKVLP 310 ********************************************************************* PP TIGR01344 275 drdavtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGt 343 +r +vtm+++fl+ays+lliqtchrrga+a+GGmaa+iPi +d+aane+a+++vradk re+++GhdGt lcl|NCBI__GCF_001431535.1:WP_057509261.1 311 ERGQVTMTQPFLKAYSELLIQTCHRRGAHAMGGMAAQIPIGNDAAANEQAMARVRADKLREVTAGHDGT 379 ********************************************************************* PP TIGR01344 344 wvahPdlvevalevfdevlgepnqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlr 412 wvahP+l++va+++fde+++ +nq +++r +dv++ + +l++ + +s + +G+ n++v +ry++awl+ lcl|NCBI__GCF_001431535.1:WP_057509261.1 380 WVAHPALIPVAMAIFDEHMPGANQQQVLR-QDVRVDRDQLIARPPGSISRAGFEGNVEVCVRYLAAWLD 447 ***************************99.9************************************** PP TIGR01344 413 GsGavpiynlmedaataeisraqlwqwikh.GvvledGekvtselvrdllkeeleklkkesgkeeyaka 480 G+G+vpi+nlmedaataeisr+qlwqw+++ G+ l+dG + ++l+ ++l++ ++l + ++ + + lcl|NCBI__GCF_001431535.1:WP_057509261.1 448 GNGCVPIHNLMEDAATAEISRSQLWQWLHTpGQQLDDGTAIDAALLDNALAQLPARLGDRATLP--GGG 514 ****************************9669*************************9996665..599 PP TIGR01344 481 rleeaaellerlvlseeledfltlpaydel 510 r++ea ll +l+ ++el+dfltlpay ++ lcl|NCBI__GCF_001431535.1:WP_057509261.1 515 RVDEAIALLAELSRADELNDFLTLPAYARI 544 ***************************886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (511 nodes) Target sequences: 1 (545 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: 00:00:00.02 # Mc/sec: 10.19 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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