Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011382757.1 AMB_RS01570 protein meaA
Query= BRENDA::Q23381 (744 letters) >lcl|NCBI__GCF_000009985.1:WP_011382757.1 AMB_RS01570 protein meaA Length = 665 Score = 403 bits (1035), Expect = e-116 Identities = 228/632 (36%), Positives = 351/632 (55%), Gaps = 14/632 (2%) Query: 94 QRPWTIRQYAGFSTVEESNKFYKENIKAGQQGLSVAFDLATHRGYDSDNPRVFGDVGMAG 153 ++PW R Y+G S+ ESNK Y+ N+ GQ GLS+AFDL T GYDSD+ G+VG G Sbjct: 15 EKPWLFRTYSGHSSAAESNKLYRTNLTKGQTGLSIAFDLPTQTGYDSDHVLAKGEVGKVG 74 Query: 154 VAVDSVEDMRQLFDGINLEKMSVSMTMNGAVVPVLAMYVVAAEEAGVSRKLLAGTIQNDI 213 V V + DM LF+GI LEKM+ SMT+N +L++Y+ AAE G +R +L GT QND+ Sbjct: 75 VPVCHLGDMMTLFEGIPLEKMNTSMTINAPAAWLLSLYIAAAERQGANRSVLNGTTQNDV 134 Query: 214 LKEFMVRNTYIYPPEPSMRIIGDIFAYTSREMPKFNSISISGYHMQEAGADAVLEMAFTI 273 +KE++ R TYI+ P+PS+++ GD+ A+T RE+PK+N +++ YH+QEAGA E+A+ + Sbjct: 135 IKEYLSRGTYIFAPQPSLKLTGDVIAFTYREVPKWNPMNVCSYHLQEAGATPEQELAYAL 194 Query: 274 ADGIQYCET--GLNAGLTIDAFAPRLSFFWGISMNFYMEIAKMRAARRLWANLIKERFSP 331 A + +T + R+SFF + F E+ KMRA LW + R+ Sbjct: 195 ATAVAVLDTVRPTVPAADFEQVVSRISFFVNAGIRFVTELCKMRAFTELWDEICVGRYGV 254 Query: 332 KSDKSMMLRTHSQTSGWSLTEQDPYNNIIRTTIEAMASVF---GGTQSLHTNSFDEALGL 388 K +K+ R Q + LTEQ P NN+ R +E +A V +++ +++EALGL Sbjct: 255 KDEKARRFRYGVQVNSLGLTEQQPENNVYRIVMEMLAVVLSKNARARAVQLPAWNEALGL 314 Query: 389 PTKFSARIARNTQIIIQEESGICNVADPWGGSYMMESLTDEIYEKALAVIKEIDELGGMA 448 P + + + Q I+ E+ + D + GS+ + + + E A + ID +GG Sbjct: 315 PRPWDQQWSLRLQQIMAYETDLLEFGDIFDGSHEITRKVEALKEGAREELARIDAMGGAV 374 Query: 449 KAVASGMTKLKIEEAAAKKQARIDAGKDVIVGVNKYRLDHEQQV-----EVLKIDNAKVR 503 AV S K K+ E+ A++ I+ G+ ++VGVNK+ + ++ +D K Sbjct: 375 SAVESSYMKQKLVESNARRIGAIETGEQIVVGVNKWTETEPSPLTTGEGSIMTVD-PKAE 433 Query: 504 EEQCAKLNHIRATRDAEKAQKALDAITEGARGNGNLMELAIEAARARCTVGEISDAMEKV 563 EQ +L RA RDA+ KAL + A N+ME +I AA A T GE + + V Sbjct: 434 AEQIERLKAFRAARDAKAVDKALAELRSAANEGRNVMEPSIAAAHAGVTTGEWAQCLRDV 493 Query: 564 FNRHAAVNRLVSGAYKSEFGETSEMSQVLERVKSFADRDGRQPRIMVAKMGQDGHDRGAK 623 F + A + A + + GE +M V +V++ + + GR+ +I+V K G DGH GA+ Sbjct: 494 FGEYRAPTGVARAAAEVK-GE--KMGAVRAKVEAVSAKLGRRVKILVGKPGLDGHSNGAE 550 Query: 624 VIATGFADLGFDVDVGPLFQTPLEAAQQAVDADVHVIGASSLAAGHLTLIPQLIGELKKL 683 IA D G +V + TP + A++ VHV+G S L+ H+ L+ +++ +K Sbjct: 551 QIAVRARDAGMEVVYEGIRLTPAQIVNAALEEGVHVVGLSILSGSHVPLVTEVLERMKAA 610 Query: 684 GRPDILVVAGGVIPPQDYKELYDAGVALVFGP 715 G DI VVAGG+IPP+D K L AG A ++ P Sbjct: 611 GLSDIPVVAGGIIPPEDEKVLLAAGCARIYTP 642 Lambda K H 0.318 0.133 0.382 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: 1023 Number of extensions: 40 Number of successful extensions: 5 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: 744 Length of database: 665 Length adjustment: 39 Effective length of query: 705 Effective length of database: 626 Effective search space: 441330 Effective search space used: 441330 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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