Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate 7025793 Shewana3_2943 malate synthase (RefSeq)
Query= reanno::MR1:200654 (549 letters) >FitnessBrowser__ANA3:7025793 Length = 549 Score = 1083 bits (2802), Expect = 0.0 Identities = 536/549 (97%), Positives = 538/549 (97%) Query: 1 MTEHTLSEQQVNLTLNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTL 60 MTEHTL EQQ+N T NKATANGTLALVGNTIPGQEVIFTEGA+ALLESLCREF EVPTL Sbjct: 1 MTEHTLGEQQLNSTQNKATANGTLALVGNTIPGQEVIFTEGALALLESLCREFATEVPTL 60 Query: 61 LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL 120 LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL Sbjct: 61 LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL 120 Query: 121 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR 180 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR Sbjct: 121 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR 180 Query: 181 VRGLHLKEKHVEFNQQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA 240 VRGLHLKEKHVEFNQQSIPG LFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA Sbjct: 181 VRGLHLKEKHVEFNQQSIPGALFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA 240 Query: 241 KVFAFVEERFCLQAGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 300 KVFAFVEERFCLQ GTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT Sbjct: 241 KVFAFVEERFCLQPGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 300 Query: 301 LKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVL 360 LKRH DRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNE VL Sbjct: 301 LKRHSDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNETVL 360 Query: 361 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL 420 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL Sbjct: 361 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL 420 Query: 421 LKTCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG 480 LK CDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG Sbjct: 421 LKPCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG 480 Query: 481 KSLSNGKLVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT 540 KSLSNGK VTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT Sbjct: 481 KSLSNGKPVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT 540 Query: 541 LPGYEMLTA 549 LPGYEMLTA Sbjct: 541 LPGYEMLTA 549 Lambda K H 0.321 0.137 0.411 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: 1063 Number of extensions: 15 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: 549 Length of database: 549 Length adjustment: 36 Effective length of query: 513 Effective length of database: 513 Effective search space: 263169 Effective search space used: 263169 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: 53 (25.0 bits)
Align candidate 7025793 Shewana3_2943 (malate synthase (RefSeq))
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.28084.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-250 816.1 0.0 5e-250 815.9 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7025793 Shewana3_2943 malate synthase (R Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7025793 Shewana3_2943 malate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 815.9 0.0 5e-250 5e-250 1 510 [. 37 547 .. 37 548 .. 0.99 Alignments for each domain: == domain 1 score: 815.9 bits; conditional E-value: 5e-250 TIGR01344 1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGPvdr 77 ++t+ al++l +l+r+fa+ + lla+r+++qa++dkg+l+dflpet++ir++ wk+ ip+dlldrrveitGPv+r lcl|FitnessBrowser__ANA3:7025793 37 IFTEGALALLESLCREFATEVPTLLAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVER 113 799************************************************************************** PP TIGR01344 78 kmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprGwhlkerh 154 kmvinalna+akvf+adfeds +P+w++vveGqinl+da+rgei++t++e+gk+y+l ++ avli+r+rG+hlke+h lcl|FitnessBrowser__ANA3:7025793 114 KMVINALNANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICRVRGLHLKEKH 190 ***************************************************************************** PP TIGR01344 155 leidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGtikatvlietlp 231 +e ++++i+g+l+df++yf+hn r+ll+kG+GPyfy+Pklesh+ear+w vf + +e + l+ Gtik t lietlp lcl|FitnessBrowser__ANA3:7025793 191 VEFNQQSIPGALFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWAKVFAFVEERFCLQPGTIKCTCLIETLP 267 ***************************************************************************** PP TIGR01344 232 aafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGm 308 a+femdeilyelr ++ lncGrwdyifs+ik+lk+++++vlPdr+avtmd++fl+ays+lli+tch+rga a+GGm lcl|FitnessBrowser__ANA3:7025793 268 AVFEMDEILYELRSNIVALNCGRWDYIFSYIKTLKRHSDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGM 344 ***************************************************************************** PP TIGR01344 309 aafiPikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge..pnqldrvrledvsitaael 383 aafiP+k dpa ne++l++vr dke+ea+nGhdGtwvahP+l+++a+ +f+e++g+ +nql+ +r++d++i aael lcl|FitnessBrowser__ANA3:7025793 345 AAFIPAK-DPAQNETVLQRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQdhQNQLHITRDVDAPILAAEL 420 *******.**********************************************987789999************** PP TIGR01344 384 levkdasrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdl 460 l+ +d++rte+G+r nir++l+y+eaw++G+G+vpiy lmedaataeisra++wqwi+hG++l++G+ vt++l++d+ lcl|FitnessBrowser__ANA3:7025793 421 LKPCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHGKSLSNGKPVTKQLFKDM 497 ***************************************************************************** PP TIGR01344 461 lkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510 l eel+++kke+g+++++++++++aa lle +++s+el dfltlp+y++l lcl|FitnessBrowser__ANA3:7025793 498 LVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLTLPGYEML 547 ************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (511 nodes) Target sequences: 1 (549 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: 10.98 // [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