Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_041102365.1 SUTH_RS14010 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >NCBI__GCF_000828635.1:WP_041102365.1 Length = 214 Score = 240 bits (612), Expect = 2e-68 Identities = 125/217 (57%), Positives = 150/217 (69%), Gaps = 6/217 (2%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 M LY Y+RSSA++RVRIAL LKG+ + SVHLV+ GG+Q A++ A+NP LVP L Sbjct: 1 MKLYNYFRSSASFRVRIALALKGLDYDYASVHLVKGGGQQFAAEFKAMNPAALVPVL--- 57 Query: 61 DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120 + DG LTQSLAIIEYLDE P+ PLLPA A RA RA+AL IACEIHPLNNLRVL Y Sbjct: 58 -DDDGTVLTQSLAIIEYLDETRPQPPLLPADAAGRARARAIALAIACEIHPLNNLRVLGY 116 Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLV--RHSGRYCFGDKVTIADLCLVPQVYNA 178 L++ L V+EE KSAWY HWV TG +E L +G C GD T+AD+CLVPQ++NA Sbjct: 117 LSKTLGVSEEEKSAWYRHWVETGLATVEAMLAGDPRTGSCCHGDMPTLADICLVPQIFNA 176 Query: 179 QRFNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215 QRFN L P +MR+ C LPAFA + P Q DA Sbjct: 177 QRFNARLDHVPTVMRIHEHCLTLPAFARSVPALQPDA 213 Lambda K H 0.321 0.134 0.408 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: 179 Number of extensions: 6 Number of successful extensions: 3 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: 216 Length of database: 214 Length adjustment: 22 Effective length of query: 194 Effective length of database: 192 Effective search space: 37248 Effective search space used: 37248 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 WP_041102365.1 SUTH_RS14010 (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.15457.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-91 291.2 0.0 2.5e-91 291.0 0.0 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041102365.1 SUTH_RS14010 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000828635.1:WP_041102365.1 SUTH_RS14010 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 291.0 0.0 2.5e-91 2.5e-91 1 210 [. 2 213 .. 2 214 .] 0.99 Alignments for each domain: == domain 1 score: 291.0 bits; conditional E-value: 2.5e-91 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlA 68 klY+yfrSsas+RvRiaLaLkg+dy + +v+L+k G+q+++efka+NP++lvP+L++d g+vltqSlA lcl|NCBI__GCF_000828635.1:WP_041102365.1 2 KLYNYFRSSASFRVRIALALKGLDYDYASVHLVKGgGQQFAAEFKAMNPAALVPVLDDD-GTVLTQSLA 69 69*********************************9***********************.6******** PP TIGR01262 69 iieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiek 137 iieyL+et+p+p+Llp+d+a rar+ra+al+iac+ihPl+Nlrvl +l+++lgv+eeek++w++hw+e+ lcl|NCBI__GCF_000828635.1:WP_041102365.1 70 IIEYLDETRPQPPLLPADAAGRARARAIALAIACEIHPLNNLRVLGYLSKTLGVSEEEKSAWYRHWVET 138 ********************************************************************* PP TIGR01262 138 GlaalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahp 204 Gla++E++l+ +++g+ c+Gd +tlad+cLvpq+ nA+rf+ l+++Pt+ ri+e++ +lpaf+++ p lcl|NCBI__GCF_000828635.1:WP_041102365.1 139 GLATVEAMLAgdPRTGSCCHGDMPTLADICLVPQIFNAQRFNARLDHVPTVMRIHEHCLTLPAFARSVP 207 *********99999******************************************************* PP TIGR01262 205 enqpdt 210 + qpd+ lcl|NCBI__GCF_000828635.1:WP_041102365.1 208 ALQPDA 213 *****7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (214 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: 8.20 // [ok]
This GapMind analysis is from Sep 24 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