Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011764431.1 AZO_RS03495 methylmalonyl-CoA mutase
Query= BRENDA::A4YEG1 (553 letters) >NCBI__GCF_000061505.1:WP_011764431.1 Length = 1088 Score = 272 bits (696), Expect = 4e-77 Identities = 195/561 (34%), Positives = 292/561 (52%), Gaps = 41/561 (7%) Query: 23 KERKNKFT--TPSGIEIKTLYTP-LDLKGD---YEEKIGFPGEYPYTRGIYPNMYRGRIW 76 KE + K T + SG +I+ + P D G+ + K PG +PYT G++ G Sbjct: 531 KEIRTKLTYESLSGSKIRKVALPNFDDDGETLKFLMKENVPGSFPYTAGVFAFKREGEDP 590 Query: 77 TIRQYAGFGSAEDTNARFRKLLEAGQTG-LSTAFDLPTQLGLDPD-NELAYTEVGVVGVS 134 T R +AG G A TN RF+K+ E LSTAFD T G DPD Y ++G GVS Sbjct: 591 T-RMFAGEGDAFRTNRRFKKVSEGMPAHRLSTAFDSVTLYGCDPDLRPDIYGKIGNSGVS 649 Query: 135 MFHWKEMDIVTNQIPL--NKVSTSMTINATAMELLSMYVATA---------ESRGVSPTE 183 + +M ++ + L S SMTIN A +L+ + TA G PTE Sbjct: 650 IATLDDMKVLYDGFDLCCPTTSVSMTINGPAPIILAFFFNTALEQQLAKFKADNGRDPTE 709 Query: 184 -------------IDGTVQNDILKEYIARKNYIYPPEPSMRYAIDIIEYSYKN-IPKWHP 229 + GTVQ DILKE + I+ E +++ DI E+ +N + ++ Sbjct: 710 DEYAKIRAWTLSSVRGTVQADILKEDQGQNTCIFSTEFALKMMGDIQEFFVRNKVQNFYS 769 Query: 230 ISISGYHIREAGADAVLEVAFTLADGIEYVRRTAERGIPVDDFAPTLSFFFAGYTNLFEE 289 +SISGYHI EAGA+ + ++AFTLA+G YV RG+ +DDFAP LSFFF+ + E Sbjct: 770 VSISGYHIAEAGANPISQLAFTLANGFTYVESYLARGMHIDDFAPNLSFFFSNGMDP-EY 828 Query: 290 VAKFRAARRMWAKIMRDMFNAKKADSMTLKFHTQTGGAELTAQQPEINIIRTTIQALAAA 349 R ARR+WA M++ + A + S LK+H QT G L AQ+ + N IRTT+QAL A Sbjct: 829 TVIGRVARRIWAVAMKNKYGANER-SQKLKYHVQTSGRSLHAQEMDFNDIRTTLQALIAI 887 Query: 350 LGGTQSLHVNSYDEAVALPSEKAAKIAIRVQQIVAYESGSTETVDPLAGSYYVEWLTDEI 409 SLH N+YDEA+ P+E++ + A+ +Q I+ E G + +P GS+ VE LTD + Sbjct: 888 YDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINREWGLAKNENPNQGSFIVEELTDLV 947 Query: 410 EERAWKIIERVEGMGGMMKAVERGFPQAEIAESAYRLQKKIEEGEMIRVGVNMSYEPDWI 469 EE K E + GG++ A+E G+ + +I E + + K +G +GVN P Sbjct: 948 EEAVLKEFEAIASRGGVLGAMETGYQRGKIQEESLYYEHKKHDGSYPIIGVNTFLNPKGQ 1007 Query: 470 GTTEV--FRVNPEIRERVLTRLKKYRSERDQMKVRDSLNALRKAAENPSVNLFPYVLDAI 527 E+ R E ++ L RLK + + + + EN N+F ++DA+ Sbjct: 1008 AQQEIELARSTEEEKQSQLARLKDFHARNKAEAPKWQAKLQQTVIENG--NVFEVLVDAV 1065 Query: 528 KKGCTVGEISSTLREIWGEYK 548 + C++G+I+ L ++ G+Y+ Sbjct: 1066 RY-CSLGQITEALYKVGGQYR 1085 Lambda K H 0.317 0.134 0.390 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: 1255 Number of extensions: 56 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: 553 Length of database: 1088 Length adjustment: 41 Effective length of query: 512 Effective length of database: 1047 Effective search space: 536064 Effective search space used: 536064 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