Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate Ac3H11_2306 Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
Query= reanno::acidovorax_3H11:Ac3H11_2306 (222 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2306 Length = 222 Score = 451 bits (1161), Expect = e-132 Identities = 222/222 (100%), Positives = 222/222 (100%) Query: 1 MQLYNYFRSSASFRVRIALQIKGLAYDYLPVHLVKGEHKAPEYASRIGDALVPTLVTDGG 60 MQLYNYFRSSASFRVRIALQIKGLAYDYLPVHLVKGEHKAPEYASRIGDALVPTLVTDGG Sbjct: 1 MQLYNYFRSSASFRVRIALQIKGLAYDYLPVHLVKGEHKAPEYASRIGDALVPTLVTDGG 60 Query: 61 TALSQSMAIIEYLDETHPTPALLPATPLARARVRALAQMVACEIHPINNLRVLKYLVRDL 120 TALSQSMAIIEYLDETHPTPALLPATPLARARVRALAQMVACEIHPINNLRVLKYLVRDL Sbjct: 61 TALSQSMAIIEYLDETHPTPALLPATPLARARVRALAQMVACEIHPINNLRVLKYLVRDL 120 Query: 121 KVDEDAKNAWYRHWVRSGLEAFERQFALLAQERAAQGLAPSVLCWGDTPTLADCCLVPQI 180 KVDEDAKNAWYRHWVRSGLEAFERQFALLAQERAAQGLAPSVLCWGDTPTLADCCLVPQI Sbjct: 121 KVDEDAKNAWYRHWVRSGLEAFERQFALLAQERAAQGLAPSVLCWGDTPTLADCCLVPQI 180 Query: 181 FNGQRFNVNLDGLPLTMGAFEACMALPAFQQAQPSACPDFEA 222 FNGQRFNVNLDGLPLTMGAFEACMALPAFQQAQPSACPDFEA Sbjct: 181 FNGQRFNVNLDGLPLTMGAFEACMALPAFQQAQPSACPDFEA 222 Lambda K H 0.323 0.136 0.421 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: 297 Number of extensions: 6 Number of successful extensions: 1 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: 222 Length of database: 222 Length adjustment: 22 Effective length of query: 200 Effective length of database: 200 Effective search space: 40000 Effective search space used: 40000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 45 (21.9 bits)
Align candidate Ac3H11_2306 (Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18))
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.12953.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-79 252.3 0.0 2.2e-79 252.0 0.0 1.1 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2306 Maleylacetoacetate isomerase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2306 Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferas # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 252.0 0.0 2.2e-79 2.2e-79 1 209 [. 2 219 .. 2 221 .. 0.93 Alignments for each domain: == domain 1 score: 252.0 bits; conditional E-value: 2.2e-79 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegev 62 +lY+yfrSsas+RvRiaL++kg++y + pv+L+k Ge+k++e++++ +lvPtL++d+g+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2306 2 QLYNYFRSSASFRVRIALQIKGLAYDYLPVHLVK-GEHKAPEYASRIGDALVPTLVTDGGTA 62 69********************************.9************************** PP TIGR01262 63 ltqSlAiieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvde 124 l+qS+AiieyL+et+p+paLlp+ p +rarvrala+++ac+ihP++Nlrvl++l + l+vde lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2306 63 LSQSMAIIEYLDETHPTPALLPATPLARARVRALAQMVACEIHPINNLRVLKYLVRDLKVDE 124 ************************************************************** PP TIGR01262 125 eekkewlkhwiekGlaalEellk......ekag....afcvGdevtladvcLvpqvynAerf 176 ++k++w++hw+++Gl+a+E+ + +++g c Gd++tlad+cLvpq+ n +rf lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2306 125 DAKNAWYRHWVRSGLEAFERQFAllaqerAAQGlapsVLCWGDTPTLADCCLVPQIFNGQRF 186 *******************85443333322222333358*********************** PP TIGR01262 177 evdlaqyPtlkrieealaelpafqeahpenqpd 209 +v+l+ P+ ea+ +lpafq+a+p+ pd lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2306 187 NVNLDGLPLTMGAFEACMALPAFQQAQPSACPD 219 *****************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (222 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.36 // [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