Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_012399727.1 BPHY_RS01515 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >NCBI__GCF_000020045.1:WP_012399727.1 Length = 214 Score = 248 bits (634), Expect = 5e-71 Identities = 126/217 (58%), Positives = 157/217 (72%), Gaps = 6/217 (2%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 M LY Y+RSSA+YRVRIALNLK + E + VHL+RDGGEQ K +Y LN +VPTLV Sbjct: 1 MKLYSYFRSSASYRVRIALNLKNLPYEYVPVHLLRDGGEQFKPEYRKLNHDAIVPTLV-- 58 Query: 61 DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120 +G +TQSLAIIEYL+E +P+ LLP+ +RA+VR++ +ACEIHPLNNLRVL+Y Sbjct: 59 --DNGHVITQSLAIIEYLEETHPEPALLPSKPADRAYVRSIVQQLACEIHPLNNLRVLKY 116 Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLVR--HSGRYCFGDKVTIADLCLVPQVYNA 178 L + + V++E K AWYHHW+++GF ALE LV +G CFGD TIAD+CLVPQV+NA Sbjct: 117 LKRTVGVSDEVKDAWYHHWISSGFAALEEYLVADGRAGMLCFGDTPTIADICLVPQVFNA 176 Query: 179 QRFNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215 RFNVDL+PYP I R+ N L AFA A P Q DA Sbjct: 177 SRFNVDLSPYPTIRRICDYANSLDAFARAEPSVQPDA 213 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: 190 Number of extensions: 8 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: 214 Length adjustment: 22 Effective length of query: 194 Effective length of database: 192 Effective search space: 37248 Effective search space used: 37248 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_012399727.1 BPHY_RS01515 (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.26192.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-93 296.5 0.0 5.9e-93 296.3 0.0 1.0 1 lcl|NCBI__GCF_000020045.1:WP_012399727.1 BPHY_RS01515 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020045.1:WP_012399727.1 BPHY_RS01515 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.3 0.0 5.9e-93 5.9e-93 1 210 [. 2 213 .. 2 214 .] 0.98 Alignments for each domain: == domain 1 score: 296.3 bits; conditional E-value: 5.9e-93 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlA 68 klYsyfrSsasyRvRiaL+Lk++ ye+vpv+Ll+d Geq+k+e+++lN + vPtL+++ g+v+tqSlA lcl|NCBI__GCF_000020045.1:WP_012399727.1 2 KLYSYFRSSASYRVRIALNLKNLPYEYVPVHLLRDgGEQFKPEYRKLNHDAIVPTLVDN-GHVITQSLA 69 69*********************************************************.6******** PP TIGR01262 69 iieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiek 137 iieyLeet+pepaLlp++pa+ra vr++++ +ac+ihPl+Nlrvl++l++++gv++e k++w++hwi++ lcl|NCBI__GCF_000020045.1:WP_012399727.1 70 IIEYLEETHPEPALLPSKPADRAYVRSIVQQLACEIHPLNNLRVLKYLKRTVGVSDEVKDAWYHHWISS 138 ********************************************************************* PP TIGR01262 138 GlaalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahp 204 G+aalEe l +ag c+Gd++t+ad+cLvpqv nA rf+vdl++yPt++ri + +++l+af++a+p lcl|NCBI__GCF_000020045.1:WP_012399727.1 139 GFAALEEYLVadGRAGMLCFGDTPTIADICLVPQVFNASRFNVDLSPYPTIRRICDYANSLDAFARAEP 207 *******9977789******************************************************* PP TIGR01262 205 enqpdt 210 + qpd+ lcl|NCBI__GCF_000020045.1:WP_012399727.1 208 SVQPDA 213 *****7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (214 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: 5.20 // [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