Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS21115 AZOBR_RS21115 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__azobra:AZOBR_RS21115 Length = 717 Score = 843 bits (2179), Expect = 0.0 Identities = 444/713 (62%), Positives = 536/713 (75%), Gaps = 13/713 (1%) Query: 18 PADAARRFEELAAKA----GTGE--AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFV 71 P ++ LAAK GT E W+T E + V L+ D + ++ LD+ G PPF Sbjct: 5 PKKTQADWQTLAAKDLGANGTLEDLVWKTPEGLDVKALYTADDLEGLE-LDSLPGFPPFT 63 Query: 72 HGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPR 131 GP ATMYA +PWTIRQYAGFSTA++SNAFY+ NL AGQ GLSVAFDL THRGYDSD+PR Sbjct: 64 RGPRATMYAVKPWTIRQYAGFSTAEDSNAFYKANLKAGQMGLSVAFDLATHRGYDSDHPR 123 Query: 132 VAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQ 191 V GDVG AGVAIDS+ DM+ LF GIPLD+MSVSMTMNGAVLPILA Y+V AEEQGV ++ Sbjct: 124 VVGDVGKAGVAIDSVEDMKILFDGIPLDKMSVSMTMNGAVLPILAGYIVAAEEQGVSQDK 183 Query: 192 LAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGAT 251 L+GTIQNDILKEFMVRNTYIYPP+PSMRII++I YT+ NMPK+NSISISGYHMQEAGAT Sbjct: 184 LSGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTALNMPKFNSISISGYHMQEAGAT 243 Query: 252 ADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKL 311 A E+A+T+ADG++Y+RA S GL VD+FAPRLSFF+ IGMNFFME+AKLRAAR+LW+ L Sbjct: 244 AVQELAFTIADGLEYVRAAMSKGLPVDKFAPRLSFFFSIGMNFFMEIAKLRAARLLWSTL 303 Query: 312 VHQ-FGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDE 370 + Q F PK+ +S++LRTH QTSG SLT QD YNNV+RT IEAMAA G TQSLHTN+ DE Sbjct: 304 MKQKFDPKDARSLALRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAVLGGTQSLHTNAFDE 363 Query: 371 AIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKV 430 A+ LPT FSARIARNTQL + +ESG T V+DP GS Y+E LT LA A I +VE + Sbjct: 364 ALGLPTKFSARIARNTQLIIAEESGVTNVVDPLGGSYYIENLTHSLANAALDLINKVEDL 423 Query: 431 GGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLA 490 GGM KA++ G+PK+ IEEAAAR QAR+D + ++GVNKYR E+ +DVL +DN+ V Sbjct: 424 GGMTKAVDSGMPKLLIEEAAARRQARVDRAEEVIVGVNKYRPENPEMVDVLDIDNTAVRE 483 Query: 491 EQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSD 550 Q A+L +RA RD K +AAL+ +T AA + NLL L ++A RA ATVGE+SD Sbjct: 484 SQIARLNSVRANRDDAKCRAALEALTKAA-----TEKSGNLLALAVEATRARATVGEISD 538 Query: 551 ALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGH 610 ALEK F R+ A IR++SGVY + + +E V F EGRRPRIL+ KMGQDGH Sbjct: 539 ALEKAFTRHVAVIRSVSGVYGAAYEGDEGFKRIQEEVSAFAAEEGRRPRILVVKMGQDGH 598 Query: 611 DRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRK 670 DRG KVIAT++AD+GFDVD+GPLFQTPEE ARQAVE DVHV+GVSS A GH TLVP L + Sbjct: 599 DRGAKVIATSFADIGFDVDIGPLFQTPEEAARQAVENDVHVIGVSSQAAGHKTLVPQLVE 658 Query: 671 ELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLR 723 EL + G DIL+ GGVIP QD+D L K GA IY PGT IP++A ++ LR Sbjct: 659 ELRRQGAGDILVVCGGVIPPQDYDYLYKAGAAAIYGPGTNIPKAASDILAILR 711 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: 1346 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: 717 Length adjustment: 40 Effective length of query: 688 Effective length of database: 677 Effective search space: 465776 Effective search space used: 465776 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