Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011382757.1 AMB_RS01570 protein meaA
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000009985.1:WP_011382757.1 Length = 665 Score = 384 bits (987), Expect = e-111 Identities = 210/488 (43%), Positives = 306/488 (62%), Gaps = 11/488 (2%) Query: 83 RGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKV 142 R + W R Y+G+++A ESNK Y+ L++GQTGLS+AFDLPTQ GYDSDH LA+GEVGKV Sbjct: 14 REKPWLFRTYSGHSSAAESNKLYRTNLTKGQTGLSIAFDLPTQTGYDSDHVLAKGEVGKV 73 Query: 143 GVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQND 202 GV + L DM LF+GIPL+K++TSMTIN+ AA LL++YI AE QG ++ L GT QND Sbjct: 74 GVPVCHLGDMMTLFEGIPLEKMNTSMTINAPAAWLLSLYIAAAERQGANRSVLNGTTQND 133 Query: 203 ILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFT 262 ++KEY++RGTYIF PQPS++LT D+I + VPKWNP+++ YH++EAGA QE+A+ Sbjct: 134 VIKEYLSRGTYIFAPQPSLKLTGDVIAFTYREVPKWNPMNVCSYHLQEAGATPEQELAYA 193 Query: 263 LADGIEYVKAV--IERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFN 320 LA + + V D ++ R+SFF A F+ E+ K RA LW I + Sbjct: 194 LATAVAVLDTVRPTVPAADFEQVVSRISFFVNAGIRFVTELCKMRAFTELWDEICVGRYG 253 Query: 321 AKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVL---GGTQSLHTNSYDEALS 377 K+ ++ R+ Q LT QQPENN+ R+ ++ LA VL +++ +++EAL Sbjct: 254 VKDEKARRFRYGVQVNSLGLTEQQPENNVYRIVMEMLAVVLSKNARARAVQLPAWNEALG 313 Query: 378 LPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGM 437 LP + +LR QQI+AYE+ +++ D G++ I + + E A + + +I MGG Sbjct: 314 LPRPWDQQWSLRLQQIMAYETDLLEFGDIFDGSHEITRKVEALKEGAREELARIDAMGGA 373 Query: 438 MRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPI-----EVEILKVDPSIR 492 + A+E Y+++++ E+ + IE G++I+VGVN + EP E I+ VDP Sbjct: 374 VSAVESSYMKQKLVESNARRIGAIETGEQIVVGVNKWTETEPSPLTTGEGSIMTVDPKAE 433 Query: 493 EKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLRE 552 +QIERLK R+ RD K V +AL +LR+AA + + P I AH + T E LR+ Sbjct: 434 AEQIERLKAFRAARDAKAVDKALAELRSAANEGRNVMEPSIAAAHAGVTT-GEWAQCLRD 492 Query: 553 IWGEYRAP 560 ++GEYRAP Sbjct: 493 VFGEYRAP 500 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: 798 Number of extensions: 36 Number of successful extensions: 5 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: 665 Length adjustment: 37 Effective length of query: 526 Effective length of database: 628 Effective search space: 330328 Effective search space used: 330328 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: 53 (25.0 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