Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_026437509.1 Q392_RS20475 maleylpyruvate isomerase
Query= reanno::MR1:200836 (216 letters) >NCBI__GCF_000745855.1:WP_026437509.1 Length = 212 Score = 196 bits (497), Expect = 4e-55 Identities = 111/218 (50%), Positives = 138/218 (63%), Gaps = 10/218 (4%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKAD-YIALNPQELVPTLVV 59 M LY +WRS ++R+RIALNLKGV E L+VHL G E+H D + ALNPQ+LVP L Sbjct: 1 MKLYNFWRSGTSHRLRIALNLKGVPYEYLAVHL---GKEEHLKDAFKALNPQQLVPAL-- 55 Query: 60 DDEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQ 119 + L QS AIIE+L+E YP LLPA A R VRA+A + C+IHP+NN R+L+ Sbjct: 56 --DTGAQVLIQSPAIIEWLEEQYPTPALLPADADGRQRVRALAAIVGCDIHPINNRRILE 113 Query: 120 YLTQKLTVNEEAKSAWYHHWVATGFTALETQLV--RHSGRYCFGDKVTIADLCLVPQVYN 177 YL + +E A +AW W++ GF A E L GRY FGD T+AD LVPQV + Sbjct: 114 YLRKTFGADEAAINAWCGTWISAGFDAYEALLAVDPKRGRYSFGDTPTLADCYLVPQVES 173 Query: 178 AQRFNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215 A+RF VDLTPYP I V A C +L AF AAP Q D+ Sbjct: 174 ARRFQVDLTPYPLIRAVDAACGELDAFRRAAPAAQPDS 211 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: 187 Number of extensions: 12 Number of successful extensions: 4 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: 212 Length adjustment: 22 Effective length of query: 194 Effective length of database: 190 Effective search space: 36860 Effective search space used: 36860 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_026437509.1 Q392_RS20475 (maleylpyruvate 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.8946.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-92 295.3 0.0 1.4e-92 295.1 0.0 1.0 1 lcl|NCBI__GCF_000745855.1:WP_026437509.1 Q392_RS20475 maleylpyruvate isom Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_026437509.1 Q392_RS20475 maleylpyruvate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 295.1 0.0 1.4e-92 1.4e-92 1 210 [. 2 211 .. 2 212 .] 0.99 Alignments for each domain: == domain 1 score: 295.1 bits; conditional E-value: 1.4e-92 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAi 69 klY+++rS++s+R+RiaL+Lkg+ ye+ +v+L k+ e+ k++fkalNPq+lvP+L+++ ++vl qS Ai lcl|NCBI__GCF_000745855.1:WP_026437509.1 2 KLYNFWRSGTSHRLRIALNLKGVPYEYLAVHLGKE-EHLKDAFKALNPQQLVPALDTG-AQVLIQSPAI 68 69********************************7.**********************.6********* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekG 138 ie+Lee+yp+paLlp+d++ r+rvrala++++cdihP++N+r+l++l++++g+de++ ++w+ +wi++G lcl|NCBI__GCF_000745855.1:WP_026437509.1 69 IEWLEEQYPTPALLPADADGRQRVRALAAIVGCDIHPINNRRILEYLRKTFGADEAAINAWCGTWISAG 137 ********************************************************************* PP TIGR01262 139 laalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpe 205 ++a+E+ll+ +k+g++++Gd++tlad++Lvpqv +A+rf+vdl++yP+++++++a+ el+af++a+p+ lcl|NCBI__GCF_000745855.1:WP_026437509.1 138 FDAYEALLAvdPKRGRYSFGDTPTLADCYLVPQVESARRFQVDLTPYPLIRAVDAACGELDAFRRAAPA 206 ********9999********************************************************* PP TIGR01262 206 nqpdt 210 qpd+ lcl|NCBI__GCF_000745855.1:WP_026437509.1 207 AQPDS 211 ****7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (212 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: 5.49 // [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