Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS24250 AZOBR_RS24250 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__azobra:AZOBR_RS24250 Length = 732 Score = 998 bits (2581), Expect = 0.0 Identities = 509/726 (70%), Positives = 592/726 (81%), Gaps = 9/726 (1%) Query: 1 MSTLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEA---WETAEQIPVGTLFNEDVYKD 57 M++LP F ++ L A A A AA+ GT A W T E + V L+ Sbjct: 1 MTSLPDFSTLPLDAAVSNASPAEWSRRFAAETGTDPATALWRTPEMLDVKPLYTAADLDG 60 Query: 58 MDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAF 117 +D L G+ PF+ GPY TMY +PWT+RQYAGFSTA+ESNAFYRRNLAAGQKGLSVAF Sbjct: 61 LDHLAAMPGMAPFLRGPYPTMYVDKPWTVRQYAGFSTAQESNAFYRRNLAAGQKGLSVAF 120 Query: 118 DLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILAL 177 DL THRGYDSD+PRV GDVGMAGVAIDSI DM+ LF GIPLDQMSVSMTMNGAVLP+LA Sbjct: 121 DLATHRGYDSDHPRVTGDVGMAGVAIDSILDMKTLFDGIPLDQMSVSMTMNGAVLPVLAG 180 Query: 178 YVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNS 237 Y+V AEEQGV ++L+GTIQNDILKEFMVRNTYIYPP+PSMRIIS+IFA+TS +MPK+NS Sbjct: 181 YIVAAEEQGVSADKLSGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAFTSQHMPKFNS 240 Query: 238 ISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFME 297 ISISGYH+QEAGATAD+E+AYTLADGV+Y RAG + GL +DQFAPRLSFFW IGMNFFME Sbjct: 241 ISISGYHLQEAGATADLELAYTLADGVEYARAGLAAGLTIDQFAPRLSFFWAIGMNFFME 300 Query: 298 VAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQ 357 VAK+RA RMLWAKL+ +F PK+ KS+SLRTHSQTSGWSLTAQDV+NNV RTCIEAMA+TQ Sbjct: 301 VAKMRAGRMLWAKLIKEFAPKSDKSLSLRTHSQTSGWSLTAQDVFNNVTRTCIEAMASTQ 360 Query: 358 GHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLA 417 GHTQSLHTN+LDEA+ALPTDFSARIARNTQLFLQQESGT RVIDPW GS YVE LT +LA Sbjct: 361 GHTQSLHTNALDEALALPTDFSARIARNTQLFLQQESGTCRVIDPWGGSYYVERLTRELA 420 Query: 418 RKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPP 477 +AWGHI+EVE+ GGMAKAIE GIPKMR+EEAAARTQARIDSGRQ ++GVNKYRLE E Sbjct: 421 ARAWGHIREVEETGGMAKAIETGIPKMRVEEAAARTQARIDSGRQTVVGVNKYRLEQEEA 480 Query: 478 LDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCID 537 ++VLKVDNS V A+Q A+L +LRAERDP + + L+ +T AA D NLL L +D Sbjct: 481 IEVLKVDNSAVRAQQIAQLERLRAERDPIRCRQTLEALTNAAAAGDG-----NLLALSVD 535 Query: 538 AGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEV-KNTPEVEEARELVEEFEQAEGR 596 A RA ATVGE+SDALEKV+GR+ A+IRTI+G+Y+ EV + + + R LV EF + +GR Sbjct: 536 AIRARATVGEISDALEKVYGRHKAEIRTITGIYAGEVGRQSDAIARVRALVAEFAERDGR 595 Query: 597 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSS 656 RPRI++AKMGQDGHDRGQKVIATA+ADLGFDVDVGPLFQTPEE ARQAVE D H+VGVSS Sbjct: 596 RPRIMVAKMGQDGHDRGQKVIATAFADLGFDVDVGPLFQTPEEAARQAVENDCHIVGVSS 655 Query: 657 LAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAI 716 LA GHLTLVP L+ EL++ G DILI VGGV+P QD+D L GA I+ PGTVI E+A+ Sbjct: 656 LAAGHLTLVPQLKAELERHGAGDILIVVGGVVPPQDYDALYAAGATAIFPPGTVISEAAV 715 Query: 717 SLVKKL 722 L++ L Sbjct: 716 DLLRIL 721 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: 1448 Number of extensions: 47 Number of successful extensions: 4 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: 732 Length adjustment: 40 Effective length of query: 688 Effective length of database: 692 Effective search space: 476096 Effective search space used: 476096 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