Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate AZOBR_RS21115 AZOBR_RS21115 methylmalonyl-CoA mutase
Query= SwissProt::Q3J4D7 (709 letters) >FitnessBrowser__azobra:AZOBR_RS21115 Length = 717 Score = 1002 bits (2590), Expect = 0.0 Identities = 508/705 (72%), Positives = 591/705 (83%), Gaps = 4/705 (0%) Query: 8 WRKLAEKELKGKSP-DSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRATM 66 W+ LA K+L + L W T EG+ VK LYT DL G+E LD LPG PFTRG RATM Sbjct: 12 WQTLAAKDLGANGTLEDLVWKTPEGLDVKALYTADDLEGLE-LDSLPGFPPFTRGPRATM 70 Query: 67 YAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVGK 126 YA +PWTIRQYAGFSTAE SNAFY+ L AGQ G+SVAFDLATHRGYDSDHPRVVGDVGK Sbjct: 71 YAVKPWTIRQYAGFSTAEDSNAFYKANLKAGQMGLSVAFDLATHRGYDSDHPRVVGDVGK 130 Query: 127 AGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTIQN 186 AGVAIDS+EDMKILF+GIPL+K+SVSMTMNGAV+PILA +IV EEQGV + LSGTIQN Sbjct: 131 AGVAIDSVEDMKILFDGIPLDKMSVSMTMNGAVLPILAGYIVAAEEQGVSQDKLSGTIQN 190 Query: 187 DILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQELAY 246 DILKEFMVRNTYIYPPEPSMRIIADIIEYT+ MPKFNSISISGYHMQEAGA VQELA+ Sbjct: 191 DILKEFMVRNTYIYPPEPSMRIIADIIEYTALNMPKFNSISISGYHMQEAGATAVQELAF 250 Query: 247 TLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSE-FAP 305 T+ADG EYVRAA+++G+ VD FA RLSFFF+IGMNFFME AKLRAARLLW +M + F P Sbjct: 251 TIADGLEYVRAAMSKGLPVDKFAPRLSFFFSIGMNFFMEIAKLRAARLLWSTLMKQKFDP 310 Query: 306 KKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPTE 365 K SL LRTHCQTSGVSL EQDPYNNVIRT EAM+A LGGTQSLHTNA DEA+ LPT+ Sbjct: 311 KDARSLALRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAVLGGTQSLHTNAFDEALGLPTK 370 Query: 366 FSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKAV 425 FSARIARNTQ+I+ EE+GVT VVDPL GSYY+E+LT LA A LI +VE +GGMTKAV Sbjct: 371 FSARIARNTQLIIAEESGVTNVVDPLGGSYYIENLTHSLANAALDLINKVEDLGGMTKAV 430 Query: 426 ASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLE 485 SGMPKL IEE+AARRQA +DR E+VIVGVNKYR + +++LDIDN AVR++QIARL Sbjct: 431 DSGMPKLLIEEAAARRQARVDRAEEVIVGVNKYRPENPEMVDVLDIDNTAVRESQIARLN 490 Query: 486 KMRATRDEAACQAALDELTRRAAE-GGNLLEAAVDASRARASVGEISMAMEKVFGRHRAE 544 +RA RD+A C+AAL+ LT+ A E GNLL AV+A+RARA+VGEIS A+EK F RH A Sbjct: 491 SVRANRDDAKCRAALEALTKAATEKSGNLLALAVEATRARATVGEISDALEKAFTRHVAV 550 Query: 545 VKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFA 604 ++++SGVYGAAYEGD+GF +IQ +V +FA EEGRRPR+LVVKMGQDGHDRGAKVIAT+FA Sbjct: 551 IRSVSGVYGAAYEGDEGFKRIQEEVSAFAAEEGRRPRILVVKMGQDGHDRGAKVIATSFA 610 Query: 605 DIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEILV 664 DIGFDVD+G LFQTPEEAA+ A++NDVHV+G+SS AAGHKTL P+L+E L+ +GAG+ILV Sbjct: 611 DIGFDVDIGPLFQTPEEAARQAVENDVHVIGVSSQAAGHKTLVPQLVEELRRQGAGDILV 670 Query: 665 ICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREARS 709 +CGGVIP QDYD+L +AG AI+GPGTNIP AA IL ++R+ ++ Sbjct: 671 VCGGVIPPQDYDYLYKAGAAAIYGPGTNIPKAASDILAILRKQKA 715 Lambda K H 0.318 0.133 0.377 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: 1405 Number of extensions: 43 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: 709 Length of database: 717 Length adjustment: 39 Effective length of query: 670 Effective length of database: 678 Effective search space: 454260 Effective search space used: 454260 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