Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_012383572.1 BIND_RS02860 maleylacetoacetate isomerase
Query= reanno::acidovorax_3H11:Ac3H11_2306 (222 letters) >NCBI__GCF_000019845.1:WP_012383572.1 Length = 216 Score = 164 bits (414), Expect = 2e-45 Identities = 92/218 (42%), Positives = 123/218 (56%), Gaps = 8/218 (3%) Query: 1 MQLYNYFRSSASFRVRIALQIKGLAYDYLPVHLVKGEHKAPEYASRIGDALVPTLVTDGG 60 MQ++ ++RS ASFRVRI L +KGLA + + V++ GE + P Y + L+P L+ G Sbjct: 1 MQIFTFWRSLASFRVRIGLNLKGLAPEQIFVNIFTGELQEPAYKAVNPQGLLPALIDGDG 60 Query: 61 TALSQSMAIIEYLDETHPTPALLPATPLARARVRALAQMVACEIHPINNLRVLKYLVRDL 120 L QS+AI+EYLDETHP P LLP P RAR RALAQ+ A + H + RV ++ + Sbjct: 61 PPLVQSLAILEYLDETHPEPPLLPKDPRGRARARALAQIAAGDAHSLVTPRVRGFMAKTY 120 Query: 121 KVDEDAKNAWYRHWVRSGLEAFERQFALLAQERAAQGLAPSVLCWGDTPTLADCCLVPQI 180 +DE + W RHWV GLEA E A LAQE+ + C GD+ T+AD ++ Sbjct: 121 NIDEAGQTLWARHWVGLGLEAIE---AHLAQEKET-----GLFCHGDSVTVADISVISLA 172 Query: 181 FNGQRFNVNLDGLPLTMGAFEACMALPAFQQAQPSACP 218 Q F L+ P F+ CMAL AF A P P Sbjct: 173 VGQQLFGGTLEAYPFLSAIFDRCMALEAFATAHPLRQP 210 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: 133 Number of extensions: 6 Number of successful extensions: 2 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: 216 Length adjustment: 22 Effective length of query: 200 Effective length of database: 194 Effective search space: 38800 Effective search space used: 38800 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 WP_012383572.1 BIND_RS02860 (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.9386.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-65 205.8 0.0 3.3e-65 205.7 0.0 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012383572.1 BIND_RS02860 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012383572.1 BIND_RS02860 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 205.7 0.0 3.3e-65 3.3e-65 2 209 .. 3 211 .. 2 213 .. 0.98 Alignments for each domain: == domain 1 score: 205.7 bits; conditional E-value: 3.3e-65 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAii 70 +++++rS as+RvRi+L+Lkg++ e vn+ Ge +++++ka+NPq+l+P+L++++g l qSlAi+ lcl|NCBI__GCF_000019845.1:WP_012383572.1 3 IFTFWRSLASFRVRIGLNLKGLAPEQIFVNIFT-GELQEPAYKAVNPQGLLPALIDGDGPPLVQSLAIL 70 79*******************************.9********************************** PP TIGR01262 71 eyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGl 139 eyL+et+pep+Llpkdp rar+rala++ a d h l rv +++++ ++de+ ++ w++hw+ Gl lcl|NCBI__GCF_000019845.1:WP_012383572.1 71 EYLDETHPEPPLLPKDPRGRARARALAQIAAGDAHSLVTPRVRGFMAKTYNIDEAGQTLWARHWVGLGL 139 ********************************************************************* PP TIGR01262 140 aalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpen 206 +a+E++l+ +++g fc+Gd+vt+ad+ +++ + + f+ l++yP l++i +++ +l+af++ahp + lcl|NCBI__GCF_000019845.1:WP_012383572.1 140 EAIEAHLAqeKETGLFCHGDSVTVADISVISLAVGQQLFGGTLEAYPFLSAIFDRCMALEAFATAHPLR 208 *******978899******************************************************** PP TIGR01262 207 qpd 209 qp lcl|NCBI__GCF_000019845.1:WP_012383572.1 209 QPG 211 *96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (216 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: 6.64 // [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