Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate PP_4619 PP_4619 Maleylacetoacetate isomerase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5292 (211 letters) >FitnessBrowser__Putida:PP_4619 Length = 210 Score = 324 bits (831), Expect = 6e-94 Identities = 162/211 (76%), Positives = 177/211 (83%), Gaps = 3/211 (1%) Query: 1 MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60 MELYTYYRSTSSYRVRIALALKGL YQ+LPVNL+ GE R Y+A+NPQGRVPALRT Sbjct: 1 MELYTYYRSTSSYRVRIALALKGLAYQSLPVNLLQ---GEQRGEGYVAVNPQGRVPALRT 57 Query: 61 DEGALLVQSPAIIEYLEERYPQVPLLSADLTVRAHERGVAALIGCDIHPLHNVSVLNKLR 120 D G +LVQSPAIIEYLEE YPQ LL A RA RGVAA+IGCDIHPLHNVSVLN+LR Sbjct: 58 DGGEVLVQSPAIIEYLEEVYPQPALLPATAEARARVRGVAAIIGCDIHPLHNVSVLNRLR 117 Query: 121 QWGHDETQVTEWIGHWISQGLAAVEQLMGDDGYCFGAAPGLADVYLIPQLYAAERFNVSL 180 Q G DE QV +WIGHWISQGLAAVEQL+GD G+CFG PGLADVYLIPQLYAAERFN+ L Sbjct: 118 QAGQDEGQVNQWIGHWISQGLAAVEQLIGDHGFCFGDTPGLADVYLIPQLYAAERFNIDL 177 Query: 181 QAYPRIRRVAALAAGHPAFQQAHPANQPDTP 211 ++PRI RVAALAA HPAF +AHPA QPD+P Sbjct: 178 DSFPRILRVAALAAAHPAFAKAHPAQQPDSP 208 Lambda K H 0.320 0.137 0.419 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: 263 Number of extensions: 13 Number of successful extensions: 2 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: 210 Length adjustment: 21 Effective length of query: 190 Effective length of database: 189 Effective search space: 35910 Effective search space used: 35910 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate PP_4619 PP_4619 (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.28662.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-90 288.5 0.0 1.7e-90 288.3 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4619 PP_4619 Maleylacetoacetate isome Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4619 PP_4619 Maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.3 0.0 1.7e-90 1.7e-90 2 210 .. 3 207 .. 2 208 .. 0.98 Alignments for each domain: == domain 1 score: 288.3 bits; conditional E-value: 1.7e-90 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAiieyLeet 76 lY+y+rS++syRvRiaLaLkg++y+s pvnLl+ Geq+ e + a+NPq++vP+L++d+gevl qS AiieyLee lcl|FitnessBrowser__Putida:PP_4619 3 LYTYYRSTSSYRVRIALALKGLAYQSLPVNLLQ-GEQRGEGYVAVNPQGRVPALRTDGGEVLVQSPAIIEYLEEV 76 9********************************.9**************************************** PP TIGR01262 77 ypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellkekag 151 yp+paLlp+ +++rarvr +a++i+cdihPl+N++vl++l++ g+de + ++w+ hwi++Glaa+E+l+ + +g lcl|FitnessBrowser__Putida:PP_4619 77 YPQPALLPATAEARARVRGVAAIIGCDIHPLHNVSVLNRLRQA-GQDEGQVNQWIGHWISQGLAAVEQLIGD-HG 149 *****************************************55.99************************98.45 PP TIGR01262 152 afcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210 fc+Gd+++ladv+L+pq+y+Aerf++dl+++P++ r+++ +a++paf++ahp++qpd+ lcl|FitnessBrowser__Putida:PP_4619 150 -FCFGDTPGLADVYLIPQLYAAERFNIDLDSFPRILRVAALAAAHPAFAKAHPAQQPDS 207 .*********************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (210 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: 9.25 // [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