Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Ga0059261_3988 Ga0059261_3988 Methylmalonyl-CoA mutase, N-terminal domain/subunit
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Korea:Ga0059261_3988 Length = 712 Score = 772 bits (1993), Expect = 0.0 Identities = 414/708 (58%), Positives = 503/708 (71%), Gaps = 12/708 (1%) Query: 20 DAARRFEELAAKAGTGEAWETAEQIPVGTLFN-EDVYKDMDWLDTYAGIPPFVHGPYATM 78 DA + E K G W T E I V L+ EDV D G PF G +M Sbjct: 8 DAWKALSEKEVK-GRDLTWRTPEGIDVKPLYTAEDVTADPG----LPGFAPFTRGVRGSM 62 Query: 79 YAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGM 138 YA RPWTIRQYAGFSTA+ESNAFYRRNLAAGQKGLSVAFDL THRGYDSD+PRV GDVG Sbjct: 63 YAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVPGDVGK 122 Query: 139 AGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQN 198 AGVAIDS+ DM+ LF GIPL +MSVSMTMNGAV+PILA ++V EEQGV QL GTIQN Sbjct: 123 AGVAIDSVEDMKILFDGIPLGEMSVSMTMNGAVIPILAFFIVAGEEQGVPRAQLDGTIQN 182 Query: 199 DILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAY 258 DILKEFMVRNTYIYPP+PSMRIIS+IF YTS MPK+NSISISGYHMQEAGAT E+A+ Sbjct: 183 DILKEFMVRNTYIYPPEPSMRIISDIFGYTSREMPKFNSISISGYHMQEAGATQVQELAF 242 Query: 259 TLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPK 318 T+ADG++Y++ G + GL++D+FA RLSFF+ IGMNFFMEVAKLRAAR+LW +++ + G K Sbjct: 243 TIADGMEYVKYGVASGLDIDKFAGRLSFFFAIGMNFFMEVAKLRAARVLWHRVMTKLGAK 302 Query: 319 NPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDF 378 + +S LRTH QTSG SLT QD YNNV+RT IEAMAA G TQSLHTN+LDEAIALPTDF Sbjct: 303 DERSKMLRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAMLGGTQSLHTNALDEAIALPTDF 362 Query: 379 SARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIE 438 SARIARNTQ+ +Q+E+G T+V+DP GS YVE LT +L KAW I+ VE GGMAKA+ Sbjct: 363 SARIARNTQIVIQEETGMTKVVDPLGGSYYVEALTQELVDKAWEIIERVEAEGGMAKAVA 422 Query: 439 KGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVK 498 G PK IEEA+A T ARID G Q ++GVNKYR E P+D+L VDN V Q A++ K Sbjct: 423 AGWPKAMIEEASAATAARIDRGEQVIVGVNKYRKAEEDPIDILDVDNHAVREAQIARIKK 482 Query: 499 LRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGR 558 +++ RD K +AALD + A + NLL L ++A R AT+GE+S A+E VFGR Sbjct: 483 VKSARDEAKCQAALDALREGARGTE------NLLALAVEAARHRATLGEISLAMEDVFGR 536 Query: 559 YTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIA 618 + +SGVY E ++ V E+ GR+PR+L+AKMGQDGHDRG +++ Sbjct: 537 HGTVPTPVSGVYGGAYAEDRRWERLKDGVAATERRLGRKPRMLVAKMGQDGHDRGANLVS 596 Query: 619 TAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRP 678 +A+ DLGF+V GPLFQTP+E A A+ +V VVG SSLA GH TL+P + L GR Sbjct: 597 SAFGDLGFEVVPGPLFQTPQEAAELAIAENVDVVGASSLAAGHKTLIPQMIGHLKDAGRG 656 Query: 679 DILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASL 726 DI + GGVIP QD+ LR G I+ PGT + +A ++ L +L Sbjct: 657 DIKVIAGGVIPAQDYQFLRDAGVQAIFGPGTNLVNAAADVLTLLGHNL 704 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: 1317 Number of extensions: 52 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: 712 Length adjustment: 40 Effective length of query: 688 Effective length of database: 672 Effective search space: 462336 Effective search space used: 462336 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