Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011382757.1 AMB_RS01570 protein meaA
Query= BRENDA::Q23381 (744 letters) >NCBI__GCF_000009985.1:WP_011382757.1 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:
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