Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_02110 H281DRAFT_02110 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__Burk376:H281DRAFT_02110 Length = 1132 Score = 304 bits (779), Expect = 1e-86 Identities = 206/553 (37%), Positives = 309/553 (55%), Gaps = 41/553 (7%) Query: 40 TDDGFEIKRIYTP--ADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYAT 97 T G +++++ P D GE ++ PG +PFT GV+ T R +AG Sbjct: 584 TLSGTQLRKVALPKFVDHGEILRWLMLDNLPGYFPFTAGVFPFRRENEDPT-RMFAGEGD 642 Query: 98 AEESNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRI 154 +N+R+K LLS+G LS AFD T G + D P G+VG GV++ +L DM Sbjct: 643 PSRTNRRFK-LLSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMHA 701 Query: 155 LFDGIPL--DKVSTSMTINSTAANLLAMYILVAEEQGVSQ-------------------- 192 L+DG L + S SMTIN A +LAM+ VA +Q +++ Sbjct: 702 LYDGFDLCAPQTSVSMTINGPAPTILAMFFNVAIDQQIARQAQQLGRALSEDELAETRRM 761 Query: 193 --EKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIR 249 E +RGTVQ DILKE + T IF + S+++ DI Y E+ V + +SISGYHI Sbjct: 762 ALENVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHRVRNFYSVSISGYHIA 821 Query: 250 EAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAAR 308 EAGAN + ++A+TLA+G YV+A + RGM +D FAP LSFFF+ N E R AR Sbjct: 822 EAGANPISQLAYTLANGFTYVEAYLARGMSIDDFAPNLSFFFS--NGMDPEYTVLGRVAR 879 Query: 309 RLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLH 368 R+WA M+E + A N RS L++H QT+G +L AQ+ + N +R +QAL A+ SLH Sbjct: 880 RVWAIAMRERYGA-NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLH 938 Query: 369 TNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYI 428 TN++DEA++ PTE+SVR A+ Q II E G+ +P G++ I+ LTD + E L Sbjct: 939 TNAFDEAITTPTEESVRRAVAIQLIINREWGLAKNQNPNQGSFVIDELTDLVEEAVLAEF 998 Query: 429 EKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVEI-LKV 487 +++ + GG++ A+E GY + I + + Y+ +G IVGVN FV+ +P E + + Sbjct: 999 DRLTERGGVLGAMETGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFVSAKPHEAPTPIAL 1058 Query: 488 DPSIREKQIERLKKLR--SERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQE 545 S E++ +LK+LR R AL++L+ A +DEN+ +++ R + +L + Sbjct: 1059 ARSTEEEKQSQLKRLRDFQARHRGAAPAALERLQRAV-IDDENVFAVLMDVVR-VCSLGQ 1116 Query: 546 VTDVLREIWGEYR 558 +T L E+ G+YR Sbjct: 1117 ITHALFEVGGQYR 1129 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: 1202 Number of extensions: 60 Number of successful extensions: 7 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: 1132 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1091 Effective search space: 569502 Effective search space used: 569502 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 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