Align Probable maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_011160203.1 TX73_RS23890 maleylacetoacetate isomerase
Query= curated2:Q9KSB2 (215 letters) >NCBI__GCF_000195775.1:WP_011160203.1 Length = 218 Score = 203 bits (517), Expect = 2e-57 Identities = 101/210 (48%), Positives = 142/210 (67%), Gaps = 3/210 (1%) Query: 5 ILYGYWRSSAAYRVRIALNIKQLVYESRAVHLSREGGEQHHAEFHRLNPSELIPVLIDGE 64 +LYGY+RSSA+YRVRIALN+K ++ R VHL GEQ+ F +NP+ ++P +GE Sbjct: 11 VLYGYFRSSASYRVRIALNLKNIIVAQRYVHL--RNGEQNLEAFRWINPAGMVPYWSEGE 68 Query: 65 LCLNQSLAIIEYLDETYPAPRLIPERGAERYQVKALALDIAADIHPINNLRILQYLTAKL 124 L QSLAIIEYLDET+P P L+P+ R V+ +A +A DIHPI NLRIL+ LT +L Sbjct: 69 FNLGQSLAIIEYLDETHPEPPLLPKDPKARAIVREIAYAVACDIHPIGNLRILKRLT-EL 127 Query: 125 GVADEEKNRWYRHWIDKGFQGLEEKLRHTAGEYCVGNRLSLVDVCLVPQVYNAERFDLDM 184 GV + ++ RW + W+++GF +E +L T G + G+R +L D+C+VPQ++NA RFD D+ Sbjct: 128 GVDEVDRARWSKEWVEQGFAAIEARLAQTPGPFAYGDRPTLADICIVPQIFNARRFDADL 187 Query: 185 SRYPTLQQIAARLRALPAFAQAAPENQPDA 214 + + ++QI A L AF A P QPDA Sbjct: 188 APFERIRQIEAEAMKLDAFVAAEPGRQPDA 217 Lambda K H 0.322 0.137 0.416 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: 161 Number of extensions: 9 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: 215 Length of database: 218 Length adjustment: 22 Effective length of query: 193 Effective length of database: 196 Effective search space: 37828 Effective search space used: 37828 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_011160203.1 TX73_RS23890 (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.9037.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-84 266.9 0.0 6.7e-84 266.7 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011160203.1 TX73_RS23890 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011160203.1 TX73_RS23890 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 266.7 0.0 6.7e-84 6.7e-84 2 210 .. 12 217 .. 11 218 .] 0.99 Alignments for each domain: == domain 1 score: 266.7 bits; conditional E-value: 6.7e-84 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAii 70 lY+yfrSsasyRvRiaL+Lk+i + v+L++ Geq+ e+f+ +NP++ vP +e l qSlAii lcl|NCBI__GCF_000195775.1:WP_011160203.1 12 LYGYFRSSASYRVRIALNLKNIIVAQRYVHLRN-GEQNLEAFRWINPAGMVPYWSEGE-FNLGQSLAII 78 9********************************.9*********************95.********** PP TIGR01262 71 eyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGl 139 eyL+et+pep+Llpkdp++ra vr++a+++acdihP+ Nlr+l++l+ +lgvde ++++w+k+w+e+G+ lcl|NCBI__GCF_000195775.1:WP_011160203.1 79 EYLDETHPEPPLLPKDPKARAIVREIAYAVACDIHPIGNLRILKRLT-ELGVDEVDRARWSKEWVEQGF 146 ***********************************************.679****************** PP TIGR01262 140 aalEellkekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqp 208 aa+E+ l+++ g f+ Gd++tlad+c+vpq+ nA+rf+ dla++ ++++ie+++ +l+af +a+p +qp lcl|NCBI__GCF_000195775.1:WP_011160203.1 147 AAIEARLAQTPGPFAYGDRPTLADICIVPQIFNARRFDADLAPFERIRQIEAEAMKLDAFVAAEPGRQP 215 ********************************************************************* PP TIGR01262 209 dt 210 d+ lcl|NCBI__GCF_000195775.1:WP_011160203.1 216 DA 217 *7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (218 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: 8.11 // [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