Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate GFF3446 Psest_3511 maleylacetoacetate isomerase
Query= reanno::psRCH2:GFF3446 (219 letters) >FitnessBrowser__psRCH2:GFF3446 Length = 219 Score = 441 bits (1135), Expect = e-129 Identities = 219/219 (100%), Positives = 219/219 (100%) Query: 1 MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL 60 MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL Sbjct: 1 MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL 60 Query: 61 LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV 120 LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV Sbjct: 61 LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV 120 Query: 121 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLETFGDKLSLNDRPGYLEACLVPQVYN 180 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLETFGDKLSLNDRPGYLEACLVPQVYN Sbjct: 121 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLETFGDKLSLNDRPGYLEACLVPQVYN 180 Query: 181 ARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDAQ 219 ARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDAQ Sbjct: 181 ARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDAQ 219 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: 327 Number of extensions: 7 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: 219 Length of database: 219 Length adjustment: 22 Effective length of query: 197 Effective length of database: 197 Effective search space: 38809 Effective search space used: 38809 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 GFF3446 Psest_3511 (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.23123.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-89 284.8 0.1 2.2e-89 284.7 0.1 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3446 Psest_3511 maleylacetoacetate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3446 Psest_3511 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 284.7 0.1 2.2e-89 2.2e-89 1 210 [. 6 218 .. 6 219 .] 0.98 Alignments for each domain: == domain 1 score: 284.7 bits; conditional E-value: 2.2e-89 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkide..gevltqSlAiiey 72 +lY+y+rSsa+yRvRiaL+Lkg++y+ vpv+L+kd G+q++++++alNPq+lvP L++++ g++++qSlAi+ey lcl|FitnessBrowser__psRCH2:GFF3446 6 TLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDgGQQRAADYRALNPQQLVPLLVDEGngGARISQSLAILEY 80 59*********************************9********************99876689*********** PP TIGR01262 73 LeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellk 147 L+e +p paLlp+dp +ra+vr+la++iac+ihPl+Nlrvlq+l+++lgvd+e+k++w++hw+++Glaa+E+ l+ lcl|FitnessBrowser__psRCH2:GFF3446 81 LDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLE 155 *************************************************************************** PP TIGR01262 148 ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210 + + + d+++ + cLvpqvynA+rf++dla+yP++ +i +++++lpafq+a+pe qpd+ lcl|FitnessBrowser__psRCH2:GFF3446 156 TFGDKLSLNDRPGYLEACLVPQVYNARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218 **************************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (219 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: 5.88 // [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