Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_057508415.1 ABB28_RS09395 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >NCBI__GCF_001431535.1:WP_057508415.1 Length = 220 Score = 237 bits (605), Expect = 1e-67 Identities = 119/217 (54%), Positives = 153/217 (70%), Gaps = 6/217 (2%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 ++L+ YWRSSAAYRVRI LNLKGV+ + +VHLVR GGEQH+ Y LNPQELVPTL Sbjct: 7 IVLHTYWRSSAAYRVRIGLNLKGVAWQGHAVHLVRGGGEQHRDSYHRLNPQELVPTL--- 63 Query: 61 DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120 + G LTQS+AI+EYLDE++ + PLLP + RA VRA+A +AC+IHP+NNLRV+QY Sbjct: 64 -QHRGQVLTQSMAILEYLDEVFAEPPLLPVDPVARARVRALAQLVACDIHPINNLRVMQY 122 Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLV--RHSGRYCFGDKVTIADLCLVPQVYNA 178 L L + +A++ W HW+A G +A+ET L +G +C GD+ +AD CLVPQ+YNA Sbjct: 123 LEGPLQLAADARTQWTLHWMAEGLSAMETMLAASADTGTFCHGDQPGLADACLVPQLYNA 182 Query: 179 QRFNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215 RF +DL YP + R+ A C LPAF A PE Q DA Sbjct: 183 HRFGLDLAGYPILRRIEAACLALPAFDAARPENQPDA 219 Lambda K H 0.321 0.134 0.408 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: 166 Number of extensions: 6 Number of successful extensions: 3 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: 216 Length of database: 220 Length adjustment: 22 Effective length of query: 194 Effective length of database: 198 Effective search space: 38412 Effective search space used: 38412 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_057508415.1 ABB28_RS09395 (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.32158.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-92 293.0 0.0 6.9e-92 292.8 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508415.1 ABB28_RS09395 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508415.1 ABB28_RS09395 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.8 0.0 6.9e-92 6.9e-92 2 210 .. 9 219 .. 8 220 .] 0.98 Alignments for each domain: == domain 1 score: 292.8 bits; conditional E-value: 6.9e-92 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlAi 69 l++y+rSsa+yRvRi+L+Lkg++++ ++v+L++ Geq+++ +++lNPqelvPtL++ g+vltqS+Ai lcl|NCBI__GCF_001431535.1:WP_057508415.1 9 LHTYWRSSAAYRVRIGLNLKGVAWQGHAVHLVRGgGEQHRDSYHRLNPQELVPTLQHR-GQVLTQSMAI 76 89********************************9***********************.6********* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekG 138 +eyL+e ++ep+Llp dp +rarvrala+l+acdihP++Nlrv+q+le l+ +++++++w+ hw+++G lcl|NCBI__GCF_001431535.1:WP_057508415.1 77 LEYLDEVFAEPPLLPVDPVARARVRALAQLVACDIHPINNLRVMQYLEGPLQLAADARTQWTLHWMAEG 145 ********************************************************************* PP TIGR01262 139 laalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpe 205 l+a+E++l+ + +g+fc+Gd+++lad cLvpq+ynA+rf++dla yP+l+rie+a+ +lpaf++a+pe lcl|NCBI__GCF_001431535.1:WP_057508415.1 146 LSAMETMLAasADTGTFCHGDQPGLADACLVPQLYNAHRFGLDLAGYPILRRIEAACLALPAFDAARPE 214 ********987889******************************************************* PP TIGR01262 206 nqpdt 210 nqpd+ lcl|NCBI__GCF_001431535.1:WP_057508415.1 215 NQPDA 219 ****7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (220 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: 6.49 // [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