Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_012757749.1 RLEG_RS11230 maleylacetoacetate isomerase
Query= reanno::psRCH2:GFF3446 (219 letters) >NCBI__GCF_000023185.1:WP_012757749.1 Length = 211 Score = 165 bits (417), Expect = 7e-46 Identities = 101/215 (46%), Positives = 126/215 (58%), Gaps = 15/215 (6%) Query: 5 LTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPLLVDE 64 + LY SSA RVRIAL LKGL +PV ++ + + R A YR++NPQ LVP L+ + Sbjct: 1 MKLYQNEISSATSRVRIALALKGLTAEALPVGILGEDSESRQAGYRSVNPQGLVPALLTD 60 Query: 65 GNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYL 124 G I+QSLAI+EYLDE+ P P LLP RA RS+A+ IA EIH L R+ +L Sbjct: 61 S--GVLITQSLAIVEYLDEIKPEPPLLPDTAEGRALARSIALAIAAEIHALLPPRIGLHL 118 Query: 125 SAELGVDDEAKNAWYRHWVSQGLAAVE-------QGLETFGDKLSLNDRPGYLEACLVPQ 177 D +A AW RHWV +G+AAVE QG F D+PG E L PQ Sbjct: 119 GKVFQADADAITAWNRHWVGEGMAAVEAMIAGRRQGAFAFA------DQPGIAEIFLFPQ 172 Query: 178 VYNARRFACDLAAYPRILEIVARCETLPAFQQAAP 212 +ARR DLA +P I EIVAR E +PAFQ+ AP Sbjct: 173 AISARRLGFDLARWPNIAEIVARLEAIPAFQENAP 207 Lambda K H 0.321 0.137 0.412 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: 140 Number of extensions: 5 Number of successful extensions: 4 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: 219 Length of database: 211 Length adjustment: 22 Effective length of query: 197 Effective length of database: 189 Effective search space: 37233 Effective search space used: 37233 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 WP_012757749.1 RLEG_RS11230 (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.29139.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-63 200.6 0.0 1.3e-63 200.5 0.0 1.0 1 lcl|NCBI__GCF_000023185.1:WP_012757749.1 RLEG_RS11230 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_012757749.1 RLEG_RS11230 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.5 0.0 1.3e-63 1.3e-63 2 205 .. 3 208 .. 2 211 .] 0.97 Alignments for each domain: == domain 1 score: 200.5 bits; conditional E-value: 1.3e-63 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlAi 69 lY+ Ssa+ RvRiaLaLkg++ e+ pv +l + e +++ ++++NPq+lvP+L +d g +tqSlAi lcl|NCBI__GCF_000023185.1:WP_012757749.1 3 LYQNEISSATSRVRIALALKGLTAEALPVGILGEdSESRQAGYRSVNPQGLVPALLTDSGVLITQSLAI 71 788888************************99887999******************************* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekG 138 +eyL+e pep+Llp+ ++ ra +r++al+ia++ih l r+ l + +++d+++ ++w +hw+ +G lcl|NCBI__GCF_000023185.1:WP_012757749.1 72 VEYLDEIKPEPPLLPDTAEGRALARSIALAIAAEIHALLPPRIGLHLGKVFQADADAITAWNRHWVGEG 140 ********************************************************************* PP TIGR01262 139 laalEellk.ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpe 205 +aa+E++++ +++gaf++ d++++a+++L pq +A+r++ dla++P + +i ++l+++pafqe +p+ lcl|NCBI__GCF_000023185.1:WP_012757749.1 141 MAAVEAMIAgRRQGAFAFADQPGIAEIFLFPQAISARRLGFDLARWPNIAEIVARLEAIPAFQENAPA 208 *********999***************************************************99886 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.83 // [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