Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate 18042 b4014 malate synthase (NCBI)
Query= ecocyc::MALATE-SYNTHASE (533 letters) >FitnessBrowser__Keio:18042 Length = 533 Score = 1080 bits (2794), Expect = 0.0 Identities = 533/533 (100%), Positives = 533/533 (100%) Query: 1 MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN 60 MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN Sbjct: 1 MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN 60 Query: 61 GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED 120 GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED Sbjct: 61 GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED 120 Query: 121 SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180 SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR Sbjct: 121 SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180 Query: 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR 240 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR Sbjct: 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR 240 Query: 241 GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA 300 GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA Sbjct: 241 GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA 300 Query: 301 VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG 360 VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG Sbjct: 301 VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG 360 Query: 361 HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA 420 HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA Sbjct: 361 HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA 420 Query: 421 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR 480 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR Sbjct: 421 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR 480 Query: 481 QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA 533 QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA Sbjct: 481 QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA 533 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: 1086 Number of extensions: 27 Number of successful extensions: 1 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: 533 Length adjustment: 35 Effective length of query: 498 Effective length of database: 498 Effective search space: 248004 Effective search space used: 248004 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 18042 b4014 (malate synthase (NCBI))
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.14192.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-254 831.2 0.0 1.3e-254 831.1 0.0 1.0 1 lcl|FitnessBrowser__Keio:18042 b4014 malate synthase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:18042 b4014 malate synthase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 831.1 0.0 1.3e-254 1.3e-254 1 510 [. 24 532 .. 24 533 .] 0.99 Alignments for each domain: == domain 1 score: 831.1 bits; conditional E-value: 1.3e-254 TIGR01344 1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGPvdrkm 79 +lt ea+efl+el +f+++r++lla+r ++q +d+g+l+df+ et++ir++dwk+ ipadl drrveitGPv+rkm lcl|FitnessBrowser__Keio:18042 24 ILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKM 102 79***************************************************************************** PP TIGR01344 80 vinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprGwhlkerhleid 158 vinalna++kvf+adfeds +P w++v++Gqinl+da++g+i++t+ e+gk y+lk++ avli+r+rG+hl+e+h++ lcl|FitnessBrowser__Keio:18042 103 VINALNANVKVFMADFEDSLAPDWNKVIDGQINLRDAVNGTISYTN-EAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180 *********************************************7.99****************************** PP TIGR01344 159 gkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGtikatvlietlpaafemd 237 g+ai+gsl+df+lyffhn ++ll+kG+GPyfylPk +s++ea +w++vf +a++ ++lprGtikat+lietlpa+f+md lcl|FitnessBrowser__Keio:18042 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLPAVFQMD 259 ******************************************************************************* PP TIGR01344 238 eilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGmaafiPikd 316 eil+ lr+h++GlncGrwdyifs+ik+lk+ +++vlPdr+avtmdk+flnays+lli+tch+rgafa+GGmaafiP+k lcl|FitnessBrowser__Keio:18042 260 EILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSK- 337 ******************************************************************************. PP TIGR01344 317 dpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge.pnqldrvrledvsitaaellevkdasrtee 394 d++ n+++l+kv+adk +ea+nGhdGtw+ahP+l+++a++vf+++lg+ +nql+++r++d++ita +ll+ +d++rtee lcl|FitnessBrowser__Keio:18042 338 DEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAMAVFNDILGSrKNQLEVMREQDAPITADQLLAPCDGERTEE 416 999********************************************99****************************** PP TIGR01344 395 GlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdllkeeleklkkesg 473 G+r nirv+++yieaw++G+G+vpiy lmedaataeisr+++wqwi+h ++l++G+ vt++l+r++l ee++ +++e+g lcl|FitnessBrowser__Keio:18042 417 GMRANIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFRQMLGEEMKVIASELG 495 ******************************************************************************* PP TIGR01344 474 keeyakarleeaaellerlvlseeledfltlpaydel 510 +e+++++r++ aa+l+e++++s+el dfltlp+y l lcl|FitnessBrowser__Keio:18042 496 EERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLL 532 **********************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (511 nodes) Target sequences: 1 (533 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: 8.66 // [ok]
This GapMind analysis is from Sep 17 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