Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate GFF991 PS417_05025 maleylacetoacetate isomerase
Query= reanno::pseudo5_N2C3_1:AO356_16835 (211 letters) >FitnessBrowser__WCS417:GFF991 Length = 213 Score = 354 bits (909), Expect = e-103 Identities = 171/211 (81%), Positives = 182/211 (86%) Query: 1 MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60 MELYTYYRSTSSYRVRIALALKGLD+ A+PVNL+ GG HRQP YLAINPQGRVPALRT Sbjct: 1 MELYTYYRSTSSYRVRIALALKGLDFTAVPVNLLVPAGGAHRQPEYLAINPQGRVPALRT 60 Query: 61 DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR 120 +EG LL+QSPAIIEYL+ERYPQ PLLS DLA RAHER VA++IGCDIHPLHN S N LR Sbjct: 61 EEGELLIQSPAIIEYLDERYPQAPLLSRDLATRAHERAVASIIGCDIHPLHNSSTQNLLR 120 Query: 121 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL 180 QWGHDEAQ+ EWIGHWISQGL AVEQLIGD G+CFG PGLAD FLIPQLYAAERF V L Sbjct: 121 QWGHDEAQLLEWIGHWISQGLGAVEQLIGDQGFCFGEQPGLADTFLIPQLYAAERFKVPL 180 Query: 181 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP 211 YPRI RVAALAA HPAF +AHPA QPDTP Sbjct: 181 ASYPRIGRVAALAAQHPAFVRAHPANQPDTP 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: 260 Number of extensions: 10 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: 213 Length adjustment: 21 Effective length of query: 190 Effective length of database: 192 Effective search space: 36480 Effective search space used: 36480 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 GFF991 PS417_05025 (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.32470.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-84 268.2 0.0 2.8e-84 268.0 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF991 PS417_05025 maleylacetoacetate i Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF991 PS417_05025 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.0 0.0 2.8e-84 2.8e-84 2 210 .. 3 210 .. 2 211 .. 0.97 Alignments for each domain: == domain 1 score: 268.0 bits; conditional E-value: 2.8e-84 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd..GeqkkeefkalNPqelvPtLkidegevltqSlAiieyLee 75 lY+y+rS++syRvRiaLaLkg+d+++vpvnLl G+++++e+ a+NPq++vP+L+++ege l qS AiieyL+e lcl|FitnessBrowser__WCS417:GFF991 3 LYTYYRSTSSYRVRIALALKGLDFTAVPVNLLVPagGAHRQPEYLAINPQGRVPALRTEEGELLIQSPAIIEYLDE 78 9******************************976679*************************************** PP TIGR01262 76 typepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellkekag 151 +yp+ +Ll++d a+ra++ra+a++i+cdihPl+N + ++ll+ ++g+de++ ew+ hwi++Gl a+E+l+ + +g lcl|FitnessBrowser__WCS417:GFF991 79 RYPQAPLLSRDLATRAHERAVASIIGCDIHPLHNSSTQNLLR-QWGHDEAQLLEWIGHWISQGLGAVEQLIGD-QG 152 ************************************999999.89**************************98.45 PP TIGR01262 152 afcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210 fc+G++++lad +L+pq+y+Aerf+v la+yP++ r+++ +a++paf +ahp+nqpdt lcl|FitnessBrowser__WCS417:GFF991 153 -FCFGEQPGLADTFLIPQLYAAERFKVPLASYPRIGRVAALAAQHPAFVRAHPANQPDT 210 .*********************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (213 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.14 // [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