Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate AO356_16835 AO356_16835 maleylacetoacetate isomerase
Query= reanno::pseudo5_N2C3_1:AO356_16835 (211 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16835 Length = 211 Score = 429 bits (1102), Expect = e-125 Identities = 211/211 (100%), Positives = 211/211 (100%) Query: 1 MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60 MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT Sbjct: 1 MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60 Query: 61 DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR 120 DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR Sbjct: 61 DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR 120 Query: 121 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL 180 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL Sbjct: 121 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL 180 Query: 181 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP 211 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP Sbjct: 181 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP 211 Lambda K H 0.321 0.138 0.422 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: 317 Number of extensions: 5 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: 211 Length of database: 211 Length adjustment: 21 Effective length of query: 190 Effective length of database: 190 Effective search space: 36100 Effective search space used: 36100 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate AO356_16835 AO356_16835 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))
# 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/TIGR01262.hmm # target sequence database: /tmp/gapView.20280.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01262 [M=211] Accession: TIGR01262 Description: maiA: maleylacetoacetate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-88 279.6 0.0 8.6e-88 279.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 AO356_16835 maleylacetoacetate i Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 AO356_16835 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 279.5 0.0 8.6e-88 8.6e-88 2 210 .. 3 210 .. 2 211 .] 0.98 Alignments for each domain: == domain 1 score: 279.5 bits; conditional E-value: 8.6e-88 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd..GeqkkeefkalNPqelvPtLkidegev 62 lY+y+rS++syRvRiaLaLkg+dy++ pvnL++ Ge++++++ a+NPq++vP+L++deg+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 3 LYTYYRSTSSYRVRIALALKGLDYQALPVNLIAApgGEHRQPAYLAINPQGRVPALRTDEGAL 65 9*******************************98889************************** PP TIGR01262 63 ltqSlAiieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdee 125 l qS AiieyLee+yp+++Ll++d a ra++r +a+li+cdihPl+N++vl++l+ ++g+de+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 66 LVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR-QWGHDEA 127 ******************************************************9.89***** PP TIGR01262 126 ekkewlkhwiekGlaalEellkekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkr 188 + +ew+ hwi++Glaa+E+l+ + g +c+G+ ++ladv+L+pq+y+Aerf+v+l+ yP+++r lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 128 QVTEWIGHWISQGLAAVEQLIGD-DG-YCFGALPGLADVFLIPQLYAAERFNVSLQGYPRIRR 188 *********************98.45.************************************ PP TIGR01262 189 ieealaelpafqeahpenqpdt 210 +++ +a +pafq+ahp++qpdt lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 189 VAALAAVHPAFQQAHPAKQPDT 210 *********************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (211 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.49 // [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