Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_076578503.1 BB347_RS03070 methylmalonyl-CoA mutase family protein
Query= BRENDA::P22033 (750 letters) >NCBI__GCF_001971705.1:WP_076578503.1 Length = 566 Score = 463 bits (1191), Expect = e-134 Identities = 242/550 (44%), Positives = 352/550 (64%), Gaps = 25/550 (4%) Query: 53 GKNPEDLIWHTPEGISIKPLYSKRDTMDLP--EEL--PGVKPFTRGPYPTMYTFRPWTIR 108 G+ ED T I + LY+ D DL E+L PG +P+TRGPYPTMY R WT+R Sbjct: 30 GERQEDFA--TVSNIDVDRLYTPEDVADLDYLEDLGFPGEEPYTRGPYPTMYRGRTWTMR 87 Query: 109 QYAGFSTVEESNKFYKDNIKAGQQGLSVAFDLATHRGYDSDNPRVRGDVGMAGVAIDTVE 168 Q+AGF T EE+N+ + I GQ GLSVAFD+ T G DSD+ G++G GVA+DT+ Sbjct: 88 QFAGFGTAEETNERFHYLIDEGQTGLSVAFDMPTLMGLDSDDRMSEGEIGKEGVAVDTLR 147 Query: 169 DTKILFDGIPLEKMSVSMTMNGAVIPVLANFIVTGEEQGVPKEKLTGTIQNDILKEFMVR 228 D +ILFDGI LE++S S T+N + + A ++ ++QGVP+E + GT+QND+ KEF+ + Sbjct: 148 DMEILFDGIDLEEISTSFTINPSAPVIYAMYVAMADQQGVPRENIRGTLQNDMFKEFIAQ 207 Query: 229 NTYIFPPEPSMKIIADIFEYTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGLEYS 288 ++ PPEPS+ ++ D+ E++ + P+F+ IS+SGYH++EAG+ A+ ELA+TLADG Y Sbjct: 208 KEWVVPPEPSLDLVTDVLEFSTEETPQFHPISVSGYHIREAGSTAVQELAFTLADGFAYV 267 Query: 289 RTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKMRAGRRLWAHLIEKMFQPKNSKSLLLR 348 ++ GL +DEFAPRLSFF+ +F+ EIAK RA RR++A ++++ + + +S L+ Sbjct: 268 EDAMERGLAVDEFAPRLSFFFNCHNSFFEEIAKYRAARRIYARVMDEWYDAQRDESKRLK 327 Query: 349 AHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSLHTNSFDEALGLPTVKSARIARNT 408 H QT+G SLT Q P NN+VR I+A+A V GGTQSLHTNSFDEAL LP+ + R+A T Sbjct: 328 FHTQTAGQSLTAQQPMNNVVRVTIQALAGVLGGTQSLHTNSFDEALALPSEDAVRVALRT 387 Query: 409 QIIIQEESGIPKVADPWGGSYMMECLTNDVYDAALKLINEIEEMG------GMAKAVAEG 462 Q II EESG + DP GGS+ +E LT++ + ++ + EI EMG G+ K + +G Sbjct: 388 QQIIAEESGAADIVDPMGGSFAVEALTDETEERTMRYLTEIREMGEGSMRDGVLKGIDDG 447 Query: 463 IPKLRIEECAARRQARIDSGSEVIVGVNKYQLEKEDAVEVLAIDNTSVRNRQIEKLKKIK 522 I++ + Q R++ G EV+VGVN++ LE++ + E L ID T+ RQ+E+L+++K Sbjct: 448 YFLREIQDASYEYQERVERGEEVVVGVNEFTLEEDTSPETLKIDETTA-ERQLERLEQVK 506 Query: 523 SSRDQALAERCLAALTECAASGDGNILALAVDASRARCTVGEITDALKKVFGEHKANDRM 582 + RD A E L L G+ N + + V+A +A TVGEI + EH Sbjct: 507 AQRDDAAVEDALEELQRTIDRGE-NTIPVLVEAVKAYATVGEIMQVFE---DEH------ 556 Query: 583 VSGAYRQEFG 592 GAY +E G Sbjct: 557 --GAYSEEIG 564 Lambda K H 0.318 0.135 0.391 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: 961 Number of extensions: 43 Number of successful extensions: 3 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: 750 Length of database: 566 Length adjustment: 38 Effective length of query: 712 Effective length of database: 528 Effective search space: 375936 Effective search space used: 375936 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: 54 (25.4 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