Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AO353_27735 AO353_27735 isocitrate lyase
Query= reanno::pseudo1_N1B4:Pf1N1B4_4042 (441 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27735 Length = 441 Score = 885 bits (2287), Expect = 0.0 Identities = 434/441 (98%), Positives = 439/441 (99%) Query: 1 MALTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVT 60 MALTREQQIAALEKDWAENPRWKGVTR YSAADVVRLRGSVQPEHTFAKMGA+KLWNLVT Sbjct: 1 MALTREQQIAALEKDWAENPRWKGVTRTYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVT 60 Query: 61 QGAKPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120 QGAKP+FRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY Sbjct: 61 QGAKPAFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120 Query: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM Sbjct: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180 Query: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR 240 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEA+QKL AARLAADVAGTPTIILAR Sbjct: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLIAARLAADVAGTPTIILAR 240 Query: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAK 300 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAP+ADLIWCETAK Sbjct: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAK 300 Query: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL Sbjct: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360 Query: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV Sbjct: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420 Query: 421 IQGGTSSVTALTGSTEEEQFH 441 IQGG+SSVTALTGSTEEEQFH Sbjct: 421 IQGGSSSVTALTGSTEEEQFH 441 Lambda K H 0.317 0.131 0.393 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: 884 Number of extensions: 11 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: 441 Length of database: 441 Length adjustment: 32 Effective length of query: 409 Effective length of database: 409 Effective search space: 167281 Effective search space used: 167281 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 AO353_27735 AO353_27735 (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.8909.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-200 650.5 4.8 8.8e-115 370.0 0.1 2.0 2 lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 AO353_27735 isocitrate lyase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 AO353_27735 isocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.0 0.1 8.8e-115 8.8e-115 2 254 .. 10 263 .. 9 264 .. 0.97 2 ! 282.4 1.5 3.1e-88 3.1e-88 353 527 .] 264 440 .. 264 440 .. 0.99 Alignments for each domain: == domain 1 score: 370.0 bits; conditional E-value: 8.8e-115 TIGR01346 2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkesk.....ektvs 61 + ++k+W ++rw++++r ysa dvv+lrGsv++e++ ++++a+klw+++++ k ek + lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 10 AALEKDWAENPRWKGVTRTYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAKpafrpEKDFV 74 5689**********************************************9986544444799** PP TIGR01346 62 ktlGaldpvqvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfh 125 +++Gal+++q++qq+ka ++a+ylsGWqv++d+n +++++Pd+++yP+d+vP++v+r++++++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 75 NCMGALTGGQAVQQVKAgIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKRINNSFRRA 139 ***************************************************************** PP TIGR01346 126 drkqkearskakdeeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlss 190 d++q++a++++ de yidy+ Pivada+aGfGGvl++++l+k +ie+Gaagvh+edql+s lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 140 DQIQWKAGKNPGDE-----GYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGVHFEDQLAS 199 ***********999.....7********************************************* PP TIGR01346 191 ekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254 +kkCGh++Gkvlvp+qe++++l+aarlaadv+g++t+++artda+aa+l+tsd+d++d++f++G lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 200 VKKCGHMGGKVLVPTQEAIQKLIAARLAADVAGTPTIILARTDANAADLLTSDCDPYDQPFVTG 263 ***************************************************************9 PP == domain 2 score: 282.4 bits; conditional E-value: 3.1e-88 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsP 417 ert+eGfy+v++g+++ai+r+ a+aPyadl+W+et++Pdl+ea++fae++k+++Pd+ll+yn+sP lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 264 ERTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAEAIKKEYPDQLLSYNCSP 328 7**************************************************************** PP TIGR01346 418 sfnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqre 482 sfnW+k+l+d +i+kf++el+++Gyk+qfitlaG+h ++ ++f+la+d+a++ m+ayv+ +q++e lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 329 SFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMFNLAHDYARNDMTAYVK-LQEQE 392 **********************************************************8.***** PP TIGR01346 483 l...edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527 + +G+++++hq+e+G++yfd++++++qgG s+++al++s+ee+qf lcl|FitnessBrowser__pseudo3_N2E3:AO353_27735 393 FadaAKGYTFVAHQQEVGTGYFDDMTTVIQGGSSSVTALTGSTEEEQF 440 *98889*****************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (527 nodes) Target sequences: 1 (441 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: 00:00:00.05 # Mc/sec: 3.88 // [ok]
This GapMind analysis is from Apr 09 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