Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_004298371.1 C665_RS01390 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000310185.1:WP_004298371.1 Length = 1088 Score = 304 bits (778), Expect = 1e-86 Identities = 209/587 (35%), Positives = 320/587 (54%), Gaps = 60/587 (10%) Query: 25 KKFLEKAPERKEKFMTDD--------------------GFEIKRIYTP--ADLGEDWNYM 62 KK L+ P+ +E + D+ G +I+++ P D GE ++ Sbjct: 506 KKLLDMWPKTRELYAADEYVVKIRDKEIRTQLTSTSLSGSKIRKVALPNFEDAGETLKFL 565 Query: 63 EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTG--LSVAF 120 K PG +P+T GV+A G T R +AG A +N+R+K + S+G LS AF Sbjct: 566 MKENVPGSFPYTAGVFAFKREGEDPT-RMFAGEGDAFRTNRRFKKV-SEGMPAHRLSTAF 623 Query: 121 DLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTAANL 177 D T G D D P G++G GV+I +L DM++L+DG L S SMTIN A + Sbjct: 624 DSVTLYGCDPDLRPDIYGKIGNSGVSIATLDDMKVLYDGFDLCCPTTSVSMTINGPAPII 683 Query: 178 LAMYILVAEEQGVSQEK----------------------LRGTVQNDILKEYIARGTYIF 215 LA + A +Q V++ K +RGTVQ DILKE + T IF Sbjct: 684 LAFFFNTALDQQVTKFKADNGREPTEDELQKIKEWTLSTVRGTVQADILKEDQGQNTCIF 743 Query: 216 PPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVI 274 + ++++ DI Y + V + +SISGYHI EAGAN + ++AFTL++G YV++ + Sbjct: 744 STEFALKMMGDIQEYFVHHDVKNFYSVSISGYHIAEAGANPISQLAFTLSNGFTYVESYL 803 Query: 275 ERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFNAKNPRSMMLRFHT 333 RGM +D FAP LSFFF+ N E + R ARR+WA MK + A N RS L++H Sbjct: 804 ARGMHIDDFAPNLSFFFS--NGMDPEYSVIGRVARRIWAVAMKNKYGA-NERSQKLKYHV 860 Query: 334 QTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQI 393 QT+G +L AQ+ + N +R +QAL A+ SLHTN+YDEA++ PTE+SVR A+ Q I Sbjct: 861 QTSGRSLHAQEMDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLI 920 Query: 394 IAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEA 453 I E G+ +P GA+ IE LTD + E LK E I GG++ A+E GY + +I E Sbjct: 921 INREWGLAKNENPNQGAFIIEELTDLVEEAVLKEFEAIASRGGVLGAMETGYQRGKIQEE 980 Query: 454 AYKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVDPSIREKQIERLKKLRS--ERDNKKV 511 + Y+ + +G I+GVN F+ + + +++ S E++ +LK+L R+ + Sbjct: 981 SLYYEHKKHDGSYPIIGVNTFLNPKGQAQQEIELARSTEEEKQGQLKRLADFHARNKDQA 1040 Query: 512 QEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558 + KL+ A ++ N+ +++A R+ +L ++T+ L ++ G+YR Sbjct: 1041 PKWQAKLQQAV-IDNTNVFEVLVDAVRY-CSLGQITEALYKVGGQYR 1085 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: 1225 Number of extensions: 58 Number of successful extensions: 6 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: 1088 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1047 Effective search space: 546534 Effective search space used: 546534 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