Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 7025792 Shewana3_2942 isocitrate lyase (RefSeq)
Query= reanno::MR1:200655 (440 letters) >FitnessBrowser__ANA3:7025792 Length = 440 Score = 874 bits (2258), Expect = 0.0 Identities = 433/440 (98%), Positives = 437/440 (99%) Query: 1 MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW 60 MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW Sbjct: 1 MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW 60 Query: 61 DLVNGGSKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA 120 DLVNGG+KKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA Sbjct: 61 DLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA 120 Query: 121 NSVPAVVSRINNSFRRADQIQWSNGVNPEDENFVDYFLPIIADAEAGFGGVLNAFELMKS 180 NSVPAVV+RINNSFRRADQIQWSNGVNPE+ENFVDYFLPIIADAEAGFGGVLNAFELMKS Sbjct: 121 NSVPAVVARINNSFRRADQIQWSNGVNPEEENFVDYFLPIIADAEAGFGGVLNAFELMKS 180 Query: 181 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD 240 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD Sbjct: 181 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD 240 Query: 241 ANAADLLTSDCDPYDRDFVTGERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPD 300 ANAADLLTSDCDPYDRDFVTGERT+EGFYRV AGLDQAISRGLAYAPYADLIWCETAKPD Sbjct: 241 ANAADLLTSDCDPYDRDFVTGERTSEGFYRVKAGLDQAISRGLAYAPYADLIWCETAKPD 300 Query: 301 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQALSDMGYKYQFITLAG 360 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQ LSDMGYKYQFITLAG Sbjct: 301 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMGYKYQFITLAG 360 Query: 361 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV 420 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV Sbjct: 361 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV 420 Query: 421 IQGGHSSVTALTGSTEEEQF 440 IQGG SSVTALTGSTEEEQF Sbjct: 421 IQGGQSSVTALTGSTEEEQF 440 Lambda K H 0.317 0.132 0.390 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: 870 Number of extensions: 25 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: 440 Length of database: 440 Length adjustment: 32 Effective length of query: 408 Effective length of database: 408 Effective search space: 166464 Effective search space used: 166464 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 7025792 Shewana3_2942 (isocitrate lyase (RefSeq))
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.19848.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-209 680.3 6.2 6.2e-118 380.4 0.1 2.0 2 lcl|FitnessBrowser__ANA3:7025792 Shewana3_2942 isocitrate lyase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7025792 Shewana3_2942 isocitrate lyase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.4 0.1 6.2e-118 6.2e-118 2 254 .. 14 261 .. 13 262 .. 0.98 2 ! 302.5 2.1 2.4e-94 2.4e-94 353 527 .] 262 440 .] 262 440 .] 1.00 Alignments for each domain: == domain 1 score: 380.4 bits; conditional E-value: 6.2e-118 TIGR01346 2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka 78 + i+k+W ++rw++++r+y+a++vv lrGs+ +e+++++++a+klw++++ k k+++++lGal+++q++qqaka lcl|FitnessBrowser__ANA3:7025792 14 DAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLWDLVNGGAK-KGYVNSLGALTGGQAVQQAKA 89 5799**********************************************99877.6******************** PP TIGR01346 79 .ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPiv 154 ++a+ylsGWqv++danl++ ++Pd+++yPa++vP++v r++++++++d++q++++ ++++e ++dy++Pi+ lcl|FitnessBrowser__ANA3:7025792 90 gIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAVVARINNSFRRADQIQWSNGVNPEEE-----NFVDYFLPII 161 ********************************************************999887.....69******** PP TIGR01346 155 adadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvar 231 ada+aGfGGvl++f+l+k +i++Gaagvh+edql+s+kkCGh++Gkvlvp+qe+v++lvaarlaadv gvetl++ar lcl|FitnessBrowser__ANA3:7025792 162 ADAEAGFGGVLNAFELMKSMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIAR 238 ***************************************************************************** PP TIGR01346 232 tdaeaatlitsdvdardhefivG 254 tda+aa+l+tsd+d++d++f++G lcl|FitnessBrowser__ANA3:7025792 239 TDANAADLLTSDCDPYDRDFVTG 261 **********************9 PP == domain 2 score: 302.5 bits; conditional E-value: 2.4e-94 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaledde 429 ert+eGfyrvk+g+++ai+r+ a+aPyadl+W+et++Pdleea++fae++++++Pd+llayn+sPsfnW+k+l+d + lcl|FitnessBrowser__ANA3:7025792 262 ERTSEGFYRVKAGLDQAISRGLAYAPYADLIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDAT 338 7**************************************************************************** PP TIGR01346 430 ikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvlkhqkesGaeyfd 502 i++f++el+d+Gyk+qfitlaG+h +++++fdla+d+a+ eGmk+yvekvq+ e+ ++G+++++hq+e+G++yfd lcl|FitnessBrowser__ANA3:7025792 339 IARFQQELSDMGYKYQFITLAGIHNMWYNMFDLAYDYARgEGMKHYVEKVQEVEFaaaKKGYTFVAHQQEVGTGYFD 415 ********************************************************999****************** PP TIGR01346 503 qllklvqgGvsataalaksveedqf 527 q+++++qgG s+++al++s+ee+qf lcl|FitnessBrowser__ANA3:7025792 416 QVTTVIQGGQSSVTALTGSTEEEQF 440 ************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (527 nodes) Target sequences: 1 (440 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: 3.66 // [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