Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_027459091.1 K420_RS0116920 isocitrate lyase
Query= reanno::acidovorax_3H11:Ac3H11_2831 (443 letters) >NCBI__GCF_000519045.1:WP_027459091.1 Length = 436 Score = 813 bits (2101), Expect = 0.0 Identities = 396/434 (91%), Positives = 418/434 (96%) Query: 10 SREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGGA 69 +REQQIAALEKDWA NPRWK VKRGYSAADVVRLRGSL E+TLA+RGA+ LW+K+NGGA Sbjct: 3 TREQQIAALEKDWAENPRWKLVKRGYSAADVVRLRGSLQPEYTLAQRGAKILWEKVNGGA 62 Query: 70 KKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV 129 KKGYVNAFGAI+AGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV Sbjct: 63 KKGYVNAFGAITAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV 122 Query: 130 RRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGAA 189 RRINNTFKRADEIQW RGINPGD+ FIDYFLPIVADAEAGFGGVLNAFELMKNMI +GAA Sbjct: 123 RRINNTFKRADEIQWSRGINPGDEGFIDYFLPIVADAEAGFGGVLNAFELMKNMIAAGAA 182 Query: 190 GVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANLI 249 GVHFEDQLAA KKCGHMGGKVLVPT+EA EKLISARFAADVMGV T++LARTDAEAANLI Sbjct: 183 GVHFEDQLAAAKKCGHMGGKVLVPTREAIEKLISARFAADVMGVPTLILARTDAEAANLI 242 Query: 250 TSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFAREF 309 TSD+D NDKPFLTGERTQEGFYRVKNGLEQ+ISRGVAYAPYADLVWCETGVPDIGFAREF Sbjct: 243 TSDYDENDKPFLTGERTQEGFYRVKNGLEQSISRGVAYAPYADLVWCETGVPDIGFAREF 302 Query: 310 AQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWFN 369 AQA+ AACPGKLLSYNCSPSFNWKKNL+D QIASFQE+LSALGYKYQFITLAGIH+NW+N Sbjct: 303 AQAIQAACPGKLLSYNCSPSFNWKKNLSDSQIASFQEELSALGYKYQFITLAGIHVNWYN 362 Query: 370 TFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVTTVIQGGSSS 429 TFQFAHAYA GEGMKHYV+MVQEPEFAAR+KGYTFVSHQQEVG GYFD+VTTVIQGGSSS Sbjct: 363 TFQFAHAYARGEGMKHYVDMVQEPEFAAREKGYTFVSHQQEVGTGYFDEVTTVIQGGSSS 422 Query: 430 VKALTGSTEEEQFH 443 VKALTGSTEEEQFH Sbjct: 423 VKALTGSTEEEQFH 436 Lambda K H 0.317 0.132 0.397 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: 823 Number of extensions: 21 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: 443 Length of database: 436 Length adjustment: 32 Effective length of query: 411 Effective length of database: 404 Effective search space: 166044 Effective search space used: 166044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_027459091.1 K420_RS0116920 (isocitrate lyase)
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))
# 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/TIGR01346.hmm # target sequence database: /tmp/gapView.3595.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01346 [M=527] Accession: TIGR01346 Description: isocit_lyase: isocitrate lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-196 637.9 2.4 5.5e-112 360.7 0.0 2.0 2 lcl|NCBI__GCF_000519045.1:WP_027459091.1 K420_RS0116920 isocitrate lyase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027459091.1 K420_RS0116920 isocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 360.7 0.0 5.5e-112 5.5e-112 2 254 .. 9 256 .. 8 258 .. 0.98 2 ! 278.0 0.7 6.8e-87 6.8e-87 353 527 .] 257 435 .. 256 435 .. 0.99 Alignments for each domain: == domain 1 score: 360.7 bits; conditional E-value: 5.5e-112 TIGR01346 2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpv 70 + ++k+W ++rw+ +kr ysa dvv+lrGs+++e +l++++ak+lw+ ++ k k++++++Ga++++ lcl|NCBI__GCF_000519045.1:WP_027459091.1 9 AALEKDWAENPRWKLVKRGYSAADVVRLRGSLQPEYTLAQRGAKILWEKVNGGAK-KGYVNAFGAITAG 76 5689**********************************************99887.6************ PP TIGR01346 71 qvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakd 138 q++qqaka l+avylsGWqv++d n+s+ ++Pd+++y +d+vP+ v+r++++++++d++q++ ++++ d lcl|NCBI__GCF_000519045.1:WP_027459091.1 77 QAMQQAKAgLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNTFKRADEIQWSRGINPGD 145 ********************************************************************9 PP TIGR01346 139 eeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqe 207 e +idy++Pivada+aGfGGvl++f+l+k +i++Gaagvh+edql++ kkCGh++Gkvlvp++e lcl|NCBI__GCF_000519045.1:WP_027459091.1 146 E-----GFIDYFLPIVADAEAGFGGVLNAFELMKNMIAAGAAGVHFEDQLAAAKKCGHMGGKVLVPTRE 209 9.....79************************************************************* PP TIGR01346 208 hvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254 ++++l++ar+aadvmgv+tl++artdaeaa+litsd d+ d++f++G lcl|NCBI__GCF_000519045.1:WP_027459091.1 210 AIEKLISARFAADVMGVPTLILARTDAEAANLITSDYDENDKPFLTG 256 **********************************************9 PP == domain 2 score: 278.0 bits; conditional E-value: 6.8e-87 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421 ert+eGfyrvk+g+e++i+r+ a+aPyadlvW+et+ Pd+ a+efa+++++ P+kll+yn+sPsfnW lcl|NCBI__GCF_000519045.1:WP_027459091.1 257 ERTQEGFYRVKNGLEQSISRGVAYAPYADLVWCETGVPDIGFAREFAQAIQAACPGKLLSYNCSPSFNW 325 8******************************************************************** PP TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edG 486 +k+l+d +i++f++el++lGyk+qfitlaG+h ++++ f++a+++a+ eGmk+yv+ vq++e+ e+G lcl|NCBI__GCF_000519045.1:WP_027459091.1 326 KKNLSDSQIASFQEELSALGYKYQFITLAGIHVNWYNTFQFAHAYARgEGMKHYVDMVQEPEFaarEKG 394 ****************************************************************999** PP TIGR01346 487 vdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527 +++++hq+e+G++yfd++++++qgG s++ al++s+ee+qf lcl|NCBI__GCF_000519045.1:WP_027459091.1 395 YTFVSHQQEVGTGYFDEVTTVIQGGSSSVKALTGSTEEEQF 435 ****************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (527 nodes) Target sequences: 1 (436 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 3.36 // [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