Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_065399519.1 BBI00_RS15060 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_001684965.1:WP_065399519.1 Length = 1115 Score = 238 bits (606), Expect = 1e-66 Identities = 150/380 (39%), Positives = 230/380 (60%), Gaps = 12/380 (3%) Query: 185 AEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMY-CAENVPKWNPISI 243 AE + + +RGTVQ DILKE A+ T IF + ++RL D+ Y E V + +SI Sbjct: 739 AEIKAKTIATVRGTVQADILKEDQAQNTCIFSTEFALRLMGDVQEYFIKEKVRNFYSVSI 798 Query: 244 SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303 SGYHI EAGAN V ++AFTLA+G YV+ + RGMD++ FAP LSFFF+ N E + Sbjct: 799 SGYHIAEAGANPVSQLAFTLANGFTYVEYYLSRGMDINDFAPNLSFFFS--NGIDPEYSV 856 Query: 304 F-RAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLG 362 R ARR+WA MK + A + RS ML++H QT+G +L AQ+ + N +R +QAL A+ Sbjct: 857 IGRVARRIWAKAMKLKYGA-DERSQMLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYD 915 Query: 363 GTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYE 422 SLHTN+YDEA++ PTE+SVR A+ Q II E G+ +PL G++ IE LTD + E Sbjct: 916 NCNSLHTNAYDEAITTPTEQSVRRAMAIQLIINKELGLAKNENPLQGSFIIEELTDLVEE 975 Query: 423 EALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFV----TDE 478 ++I + GG++ A+E Y + +I E + Y+ G+ I+GVN F+ + Sbjct: 976 AVYTEFDRITERGGVLGAMETMYQRSKIQEESMHYEWLKHTGEYPIIGVNTFLGKDGSPT 1035 Query: 479 PIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHR 538 + E+++ ++ QIE L + ++K +EAL L++AA + +NL +++A + Sbjct: 1036 VLPGEVIRSTEEEKQAQIEFLHNFQKANESKS-EEALRTLQHAAINQ-QNLFEVMMDAVK 1093 Query: 539 HLATLQEVTDVLREIWGEYR 558 + +L ++T+ L E+ G+YR Sbjct: 1094 Y-CSLGQITNALFEVGGKYR 1112 Score = 67.8 bits (164), Expect = 2e-15 Identities = 50/138 (36%), Positives = 70/138 (50%), Gaps = 7/138 (5%) Query: 59 WNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTG-LS 117 W E L PG +P+T G+Y G T R +AG E +N+R+ Y+ ++ LS Sbjct: 546 WKGQENL--PGSFPYTAGIYPFKRTGEDPT-RMFAGEGGPERTNRRFHYVSAEMPAKRLS 602 Query: 118 VAFDLPTQLGYDSDHPL-AEGEVGKVGVAIDSLWDMRILFDGIPLDKV--STSMTINSTA 174 AFD T G D P G++G GV+I +L D + L+ G L S SMTIN A Sbjct: 603 TAFDSVTLYGQDPALPPDIYGKIGNAGVSIATLDDAKKLYSGFDLVNALTSVSMTINGPA 662 Query: 175 ANLLAMYILVAEEQGVSQ 192 LLA ++ A +Q V + Sbjct: 663 PMLLAFFMNAAIDQNVEK 680 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: 1318 Number of extensions: 64 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 563 Length of database: 1115 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1074 Effective search space: 560628 Effective search space used: 560628 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: 55 (25.8 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