Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_025273328.1 HALAL_RS0107060 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000527155.1:WP_025273328.1 Length = 523 Score = 582 bits (1499), Expect = e-170 Identities = 294/509 (57%), Positives = 381/509 (74%), Gaps = 1/509 (0%) Query: 55 LGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQT 114 L E + +LG PG +P+TRG Y TMY + WTMRQYAG+ATA ESN+RY+ LL+ G T Sbjct: 16 LYESYKREPELGKPGSFPYTRGAYPTMYTTKPWTMRQYAGFATASESNQRYRELLANGST 75 Query: 115 GLSVAFDLPTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTA 174 GLSVAFDLPTQ+GYDSD +A GEVGKVGVAIDS+ DMRILF+ IPLD+VSTSMTIN+ A Sbjct: 76 GLSVAFDLPTQMGYDSDAAIAAGEVGKVGVAIDSIDDMRILFNEIPLDQVSTSMTINAPA 135 Query: 175 ANLLAMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN 234 + LL +Y LVAEEQGVS ++LRGT+QND+LKEYIARGTYIFPP+PS+RL +D YC+ Sbjct: 136 SVLLLLYQLVAEEQGVSGDQLRGTIQNDVLKEYIARGTYIFPPEPSLRLISDTFAYCSAE 195 Query: 235 VPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAH 294 +P+WN ISISGYH+ EAGA+A QE+ FTLA+GI+YV+A I+ G+D+D APRLSFFF A Sbjct: 196 MPQWNTISISGYHMAEAGADAGQELGFTLANGIQYVQAAIDAGLDIDTIAPRLSFFFVAR 255 Query: 295 NNFLEEIAKFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAI 354 ++ L E+AKFRAARRLWA++M++ F NP+S LRFHTQTAG LTAQQPE N+ RV I Sbjct: 256 SSILTEVAKFRAARRLWAHVMRDRFGTDNPKSQRLRFHTQTAGVELTAQQPEINLSRVTI 315 Query: 355 QALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIE 414 QALAAV+GGTQSLHTNS+DEAL+LPT+KS R+ALRTQQ+IA E+ + DTVDP G+Y +E Sbjct: 316 QALAAVMGGTQSLHTNSFDEALALPTDKSARLALRTQQVIANETDLTDTVDPFAGSYAVE 375 Query: 415 WLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAF 474 LTD I +A + I+ + G ++AIE+G+ + EI AY + I+ +++IVGVN + Sbjct: 376 SLTDEIEAQATELIDAVFAHGSAVKAIEQGFQKTEIERTAYATAQRIDAEEQVIVGVNKY 435 Query: 475 VTDEPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYII 534 T++ L+VDP Q++ ++ R++RDN V + L L++AA +D L P + Sbjct: 436 RTEDEEPYTPLRVDPEQEASQVKSVQATRNDRDNDVVADKLAALKSAAGTDDNILYP-MK 494 Query: 535 EAHRHLATLQEVTDVLREIWGEYRAPLIF 563 EA AT+ EV+ L E+WG Y P F Sbjct: 495 EALAAKATVGEVSGALAEVWGRYVPPETF 523 Lambda K H 0.318 0.134 0.388 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: 737 Number of extensions: 20 Number of successful extensions: 2 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: 563 Length of database: 523 Length adjustment: 35 Effective length of query: 528 Effective length of database: 488 Effective search space: 257664 Effective search space used: 257664 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: 52 (24.6 bits)
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