Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_043461124.1 H537_RS0133235 maleylacetoacetate isomerase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5292 (211 letters) >NCBI__GCF_000430725.1:WP_043461124.1 Length = 213 Score = 204 bits (520), Expect = 8e-58 Identities = 112/214 (52%), Positives = 142/214 (66%), Gaps = 9/214 (4%) Query: 1 MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60 M+LY ++RS +S+R+RIAL LKGLD +PV+L EH A+LA+NPQG VPAL Sbjct: 2 MKLYNFFRSGTSHRLRIALNLKGLDALYVPVDLRTE---EHLNEAFLALNPQGLVPALEV 58 Query: 61 DEGALLVQSPAIIEYLEERYPQVPLLSADLTVRAHERGVAALIGCDIHPLHNVSVLNKLR 120 D G +L+QSPAIIE+LEER+P+ PLL D RA R +AA++GCDIHP++N +L LR Sbjct: 59 D-GEVLIQSPAIIEWLEERHPEPPLLPRDAQARARVRALAAIVGCDIHPINNRRILEYLR 117 Query: 121 -QWGHDETQVTEWIGHWISQGLAAVEQLMGDD----GYCFGAAPGLADVYLIPQLYAAER 175 Q G DE V W G WI+ G A+E L+ D +CFG AP LADVYL+PQ+ +A R Sbjct: 118 KQLGQDEAAVNAWCGTWITAGFDAIEALLAADTARGDFCFGHAPTLADVYLVPQVESARR 177 Query: 176 FNVSLQAYPRIRRVAALAAGHPAFQQAHPANQPD 209 F V L YP IR V A AF++A PA QPD Sbjct: 178 FKVDLSPYPLIRAVDAACGELDAFRRAAPAVQPD 211 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: 177 Number of extensions: 11 Number of successful extensions: 5 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_043461124.1 H537_RS0133235 (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.29501.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-90 286.7 0.0 5.9e-90 286.5 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_043461124.1 H537_RS0133235 maleylacetoacetat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_043461124.1 H537_RS0133235 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 286.5 0.0 5.9e-90 5.9e-90 1 210 [. 3 212 .. 3 213 .] 0.99 Alignments for each domain: == domain 1 score: 286.5 bits; conditional E-value: 5.9e-90 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAi 69 klY++frS++s+R+RiaL+Lkg+d +vpv+L+ + e+ +e+f alNPq+lvP+L++d gevl qS Ai lcl|NCBI__GCF_000430725.1:WP_043461124.1 3 KLYNFFRSGTSHRLRIALNLKGLDALYVPVDLRTE-EHLNEAFLALNPQGLVPALEVD-GEVLIQSPAI 69 69********************************7.**********************.6********* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekG 138 ie+Lee++pep+Llp+d+++rarvrala++++cdihP++N+r+l++l+++lg+de++ ++w+ +wi++G lcl|NCBI__GCF_000430725.1:WP_043461124.1 70 IEWLEERHPEPPLLPRDAQARARVRALAAIVGCDIHPINNRRILEYLRKQLGQDEAAVNAWCGTWITAG 138 ********************************************************************* PP TIGR01262 139 laalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpe 205 ++a+E+ll+ +++g+fc+G ++tladv+Lvpqv +A+rf+vdl++yP+++++++a+ el+af++a+p+ lcl|NCBI__GCF_000430725.1:WP_043461124.1 139 FDAIEALLAadTARGDFCFGHAPTLADVYLVPQVESARRFKVDLSPYPLIRAVDAACGELDAFRRAAPA 207 ********987889******************************************************* PP TIGR01262 206 nqpdt 210 qpd+ lcl|NCBI__GCF_000430725.1:WP_043461124.1 208 VQPDA 212 ***96 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: 7.85 // [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