Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_01038 H281DRAFT_01038 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Burk376:H281DRAFT_01038 Length = 703 Score = 577 bits (1487), Expect = e-169 Identities = 306/652 (46%), Positives = 426/652 (65%), Gaps = 7/652 (1%) Query: 61 LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLP 120 +D+ G PFV GP+A+MY +PWTIRQYAG++ A ++N +R LA G +GLSVAFDLP Sbjct: 29 IDSMPGEAPFVRGPFASMYTQKPWTIRQYAGYAQASDTNLAFRTALAEGAQGLSVAFDLP 88 Query: 121 THRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVV 180 T RGYDSD+P V+ DVGM GVAID++ DM LF I LD++SVSMTMNGAVLP+LA ++V Sbjct: 89 TQRGYDSDDPAVSADVGMTGVAIDTVEDMTRLFEDIALDRVSVSMTMNGAVLPVLAAFIV 148 Query: 181 TAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISI 240 AEE GV QL GTIQNDILKEFMVRNT I+ P+PS+RI +++ Y N+P++N++S+ Sbjct: 149 AAEESGVGASQLRGTIQNDILKEFMVRNTSIFAPEPSLRIAADVVEYLGKNVPRFNALSV 208 Query: 241 SGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAK 300 SGYH QEAGA +E+A T+A+ YI A G+ D R+SFF+G+GM+F++E+AK Sbjct: 209 SGYHFQEAGADPVLELALTMANARKYITALAGRGMQADDVCQRMSFFFGVGMDFYVEIAK 268 Query: 301 LRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHT 360 LRAAR+LWA + G + ++ +LR H QTSGWSLTAQ NNVVRT +EA+AA G T Sbjct: 269 LRAARILWADIASASGATSDRARALRMHCQTSGWSLTAQKPMNNVVRTTVEALAAVFGGT 328 Query: 361 QSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKA 420 QSLHTN DEA++LP ++R+AR+TQL LQ E+G V+DPW+GS +E+ T ++ +KA Sbjct: 329 QSLHTNGYDEALSLPCADASRLARDTQLVLQHETGVCDVVDPWAGSYMMEKFTAEICQKA 388 Query: 421 WGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPL-D 479 + E+E+ GG+ +E G + +I +A QA I+S ++ ++GVN + + L + Sbjct: 389 LTVMAEIERRGGVVDVVESGWVRDQIHRSALNIQAEIESRKRTVVGVNDFMTGCDEDLGE 448 Query: 480 VLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAG 539 VD V Q +L ++A RDP +V+ LD +T AA + D NLL+L + Sbjct: 449 PQTVDGRRVRVLQTQRLAHIKARRDPTRVRNTLDALTRAA-----RGRDGNLLELTVACM 503 Query: 540 RAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPR 599 RA ATVGE + ALE V+ RY + + Y +++ + ++ V + + GR PR Sbjct: 504 RARATVGECTQALEAVWPRYQIGLPLLRDHYGANLESDKDWQDTCRAVADATKRLGRAPR 563 Query: 600 ILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAG 659 +L+AK+GQDGHDRG ++IA A +D GF V G +F +P +T + A V V+GVSSLAG Sbjct: 564 VLIAKLGQDGHDRGARIIAAALSDAGFAVFTGSMFASPSDTVQLAEGERVDVIGVSSLAG 623 Query: 660 GHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVI 711 L+ AL +L G I I VGG+I + LR+ G + GT I Sbjct: 624 AQNDLITALHDQLTVRGL-RIPIVVGGIIDQASQLVLRRSGVAACFPAGTPI 674 Lambda K H 0.317 0.133 0.389 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: 1067 Number of extensions: 40 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: 728 Length of database: 703 Length adjustment: 39 Effective length of query: 689 Effective length of database: 664 Effective search space: 457496 Effective search space used: 457496 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 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