Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate BPHYT_RS02085 BPHYT_RS02085 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__BFirm:BPHYT_RS02085 Length = 1298 Score = 308 bits (790), Expect = 7e-88 Identities = 205/554 (37%), Positives = 311/554 (56%), Gaps = 43/554 (7%) Query: 40 TDDGFEIKRIYTP--ADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYAT 97 T G E++++ P AD GE ++ PG +PFT GV+ T R +AG Sbjct: 750 TLSGSEVRKVSLPKFADHGEILRWLMLDNLPGYFPFTAGVFPFRRENEDPT-RMFAGEGD 808 Query: 98 AEESNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRI 154 + +N+R+K LLS+G LS AFD T G + D P G+VG GV++ +L DM+ Sbjct: 809 PQRTNRRFK-LLSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMKT 867 Query: 155 LFDGIPL--DKVSTSMTINSTAANLLAMYILVAEEQGVSQ-------------------- 192 L+DG L + S SMTIN A +LAM+ VA +Q +++ Sbjct: 868 LYDGFDLCAPETSVSMTINGPAPTILAMFFNVAIDQQIARMTQQQGRPLTHDELSATRRA 927 Query: 193 --EKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIR 249 E +RGTVQ DILKE + T IF + S+++ DI Y E+ V + +SISGYHI Sbjct: 928 ALENVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHGVRNFYSVSISGYHIA 987 Query: 250 EAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAAR 308 EAGAN + ++A+TLA+G YV+A + RGM +D FAP LSFFF+ N E R AR Sbjct: 988 EAGANPISQLAYTLANGFTYVEAYLARGMSIDDFAPNLSFFFS--NGMDPEYTVLGRVAR 1045 Query: 309 RLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLH 368 R+WA M+E + A N RS L++H QT+G +L AQ+ + N +R +QAL A+ SLH Sbjct: 1046 RIWAVAMRERYGA-NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLH 1104 Query: 369 TNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYI 428 TN++DEA++ PTE SVR A+ Q II E G+ +P G++ IE LTD + E L Sbjct: 1105 TNAFDEAITTPTEDSVRRAVAIQLIINREWGLAKNQNPNQGSFVIEELTDLVEEAVLAEF 1164 Query: 429 EKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIE----VEI 484 +++ + GG++ A+E GY + I + + Y+ +G IVGVN F++ P E + + Sbjct: 1165 DRLTERGGVLGAMETGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFLSAHPHEAPQPIAL 1224 Query: 485 LKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQ 544 + ++ Q++RL+ +S+ AL++L+ A +DEN+ +++ R + +L Sbjct: 1225 ARSTDDEKQSQLQRLRAFQSQH-RDAAPAALERLKRAV-IDDENVFAVLMDVVR-VCSLG 1281 Query: 545 EVTDVLREIWGEYR 558 ++T L E+ G+YR Sbjct: 1282 QITHALFEVGGQYR 1295 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: 1344 Number of extensions: 61 Number of successful extensions: 8 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: 1298 Length adjustment: 42 Effective length of query: 521 Effective length of database: 1256 Effective search space: 654376 Effective search space used: 654376 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: 56 (26.2 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