Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate CCNA_02459 CCNA_02459 methylmalonyl-CoA mutase alpha subunit
Query= BRENDA::Q84FZ1 (721 letters) >FitnessBrowser__Caulo:CCNA_02459 Length = 714 Score = 1070 bits (2767), Expect = 0.0 Identities = 538/713 (75%), Positives = 609/713 (85%), Gaps = 4/713 (0%) Query: 3 SRIPDFASVAYAADGFKAPPPPAGEPWMTPEGIPVKGFYGPEDREGCEGIDSFPGLPPYL 62 S PDF +A+A AP P GE W TPEG+ V + D G + FPG+ P++ Sbjct: 2 STFPDFTKIAFAE--VPAPAAPKGEAWNTPEGVAVAPAFDASDVAGLDFTGGFPGVAPFV 59 Query: 63 RGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPR 122 RGPYP MYVT PWT+RQYAGFSTAEDSNAFYRRNLAAGQ GLSVAFDLATHRGYDSDH R Sbjct: 60 RGPYPTMYVTNPWTVRQYAGFSTAEDSNAFYRRNLAAGQMGLSVAFDLATHRGYDSDHER 119 Query: 123 VSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIVAAEEQGVPPEK 182 V GDVGMAGVAIDSI DMRTLFSGIPLD+M+VSMTMNGAVLP +ALYIVAAEEQGV P+K Sbjct: 120 VKGDVGMAGVAIDSILDMRTLFSGIPLDKMSVSMTMNGAVLPILALYIVAAEEQGVSPDK 179 Query: 183 LAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISISGYHMQEAGAT 242 L+GTIQNDILKEFMVRNTYIYPP SMRIISDIF +TS NMPKFNSISISGYHMQEAGAT Sbjct: 180 LSGTIQNDILKEFMVRNTYIYPPAPSMRIISDIFAFTSANMPKFNSISISGYHMQEAGAT 239 Query: 243 QDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAKMRAARLIWAKL 302 DLELAYTLADGVEY +AG+AAG++IDQFAPRLSFFWAIGMN+FME+AKMRAARL+WA+L Sbjct: 240 ADLELAYTLADGVEYARAGVAAGMSIDQFAPRLSFFWAIGMNYFMEVAKMRAARLLWARL 299 Query: 303 VK-EFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGTQSLHTNALDE 361 +K EF+PK D+SL LRTHSQTSGWSL AQDVFNNV RTC+EAMAA G TQSLHTN+LDE Sbjct: 300 MKREFDPKDDRSLSLRTHSQTSGWSLAAQDVFNNVARTCVEAMAAVNGQTQSLHTNSLDE 359 Query: 362 ALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARAWEHIREVEAL 421 ALALPTDFSARI+RNTQLFLQ ESGTTR+ DPWGGSYYVERLT ++A +A HI EVEAL Sbjct: 360 ALALPTDFSARISRNTQLFLQMESGTTRVADPWGGSYYVERLTYELAQKALAHIEEVEAL 419 Query: 422 GGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDLLRVDNADVRA 481 GGMAKAIE G+PKLRIEEAAAR QARIDSG+Q++VG+N+YKP+ I +L+VDN VRA Sbjct: 420 GGMAKAIEQGLPKLRIEEAAARTQARIDSGKQSVVGVNRYKPEVADDIPVLKVDNGAVRA 479 Query: 482 KQIDKLKRLRAERNQADVDAALAALTKAADGEGNLLELAVNAARAKATVGEISEALEKAW 541 +Q++KL RL+AER+ A +AAL AL A G+GNLL LAV+AARAKATVGEIS ALEK + Sbjct: 480 QQLEKLARLKAERDPAATEAALTALEDGARGDGNLLALAVDAARAKATVGEISYALEKVF 539 Query: 542 GRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAKMGQDGHDRGQK 601 GRHRA+I+SI GVY +E G P + + +VEAFE+ DGRRPRIL+AKMGQDGHDRGQK Sbjct: 540 GRHRAEIKSIQGVYMKEAGN-DPTAARAKAMVEAFEQADGRRPRILIAKMGQDGHDRGQK 598 Query: 602 VIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTLVPELKAALKQE 661 VIA+AFADLGFDVDIGPLF TP EAARQAVENDVH+VG SSLAAGHLTL PELKA L ++ Sbjct: 599 VIATAFADLGFDVDIGPLFQTPAEAARQAVENDVHVVGASSLAAGHLTLAPELKAELAKQ 658 Query: 662 GRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNTRLGY 714 GRDD+++VVGGVIPP D+ AL AGA+AIFPPGTVIAEAA+ LL +LN +LGY Sbjct: 659 GRDDILMVVGGVIPPQDFQALRDAGAAAIFPPGTVIAEAAIELLEQLNRQLGY 711 Lambda K H 0.318 0.134 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: 1363 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: 721 Length of database: 714 Length adjustment: 40 Effective length of query: 681 Effective length of database: 674 Effective search space: 458994 Effective search space used: 458994 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