Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_097028688.1 CRO07_RS00240 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_900207575.1:WP_097028688.1 Length = 709 Score = 832 bits (2148), Expect = 0.0 Identities = 428/702 (60%), Positives = 526/702 (74%), Gaps = 9/702 (1%) Query: 26 EELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWT 85 +EL ++ W T E IPV L+ + +D LD G+ PF G ATMYA RPWT Sbjct: 14 KELKGRSPDSLTWNTLEGIPVKPLYTRADIEGLDHLDGVPGVAPFTRGVRATMYAGRPWT 73 Query: 86 IRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDS 145 IRQYAGFSTA+ SNAFYR+ LAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS Sbjct: 74 IRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVGKAGVAIDS 133 Query: 146 IYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFM 205 + DM+ LF GIPL+++SVSMTMNGAV+PILA ++VT EEQGV +L+GTIQNDILKEFM Sbjct: 134 VEDMKILFDGIPLEKISVSMTMNGAVIPILASFIVTGEEQGVPRAELSGTIQNDILKEFM 193 Query: 206 VRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVD 265 VRNTYIYPP+PSMRII++I YT+ MPK+NSISISGYHMQEAGA E+AYTLADG + Sbjct: 194 VRNTYIYPPEPSMRIIADIIEYTAKEMPKFNSISISGYHMQEAGANLVQELAYTLADGRE 253 Query: 266 YIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSL 325 Y+RA + G+NVD+FA RLSFF+ IGMNFFME AKLRAARMLW +++ +F PK P S+ L Sbjct: 254 YVRAAIARGMNVDEFAGRLSFFFAIGMNFFMEAAKLRAARMLWHRIMSEFEPKKPGSLML 313 Query: 326 RTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARN 385 RTH QTSG SL QD YNNV+RT EA+AA G TQSLHTN+LDEAIALPT+FSARIARN Sbjct: 314 RTHCQTSGVSLQEQDPYNNVIRTAYEALAAALGGTQSLHTNALDEAIALPTEFSARIARN 373 Query: 386 TQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMR 445 TQL LQ+E+G T+V+DP +GS YVE LT +LA KAW I+EVE +GGM KA+ G+PK+R Sbjct: 374 TQLILQEETGVTKVVDPLAGSYYVESLTNELAEKAWALIEEVEAMGGMTKAVASGMPKLR 433 Query: 446 IEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDP 505 IEE+AAR QA ID G ++GVNKYRL E P+++L +DN V Q A+L K+RA RD Sbjct: 434 IEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLEKMRATRDE 493 Query: 506 EKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRT 565 + ALD++T A NLL+ +DA RA A+VGE+S A+EKVFGR+ A+++T Sbjct: 494 AACQKALDELTRRASE------GGNLLEAAVDASRARASVGEISMAMEKVFGRHRAEVKT 547 Query: 566 ISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLG 625 +SGVY + ++ VE F + EGRRPR+L+ KMGQDGHDRG KVIATA+AD+G Sbjct: 548 LSGVYGAAYEGDDGFAAIQKDVETFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFADIG 607 Query: 626 FDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVG 685 FDVDVG LFQTPEE A+ A++ DVHVVG+SSLA GH TL P L + L G DIL+ G Sbjct: 608 FDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKAQGAGDILVICG 667 Query: 686 GVIPEQDFDELRKDGAVEIYTPGTVIPESA---ISLVKKLRA 724 GVIP+QD+D L G I+ PGT IP +A + L+++ RA Sbjct: 668 GVIPQQDYDFLYNSGVKAIFGPGTNIPSAAKQILDLIRQARA 709 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: 1316 Number of extensions: 41 Number of successful extensions: 2 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: 709 Length adjustment: 40 Effective length of query: 688 Effective length of database: 669 Effective search space: 460272 Effective search space used: 460272 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 24 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