Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_01038 H281DRAFT_01038 methylmalonyl-CoA mutase
Query= reanno::PS:Dsui_0519 (721 letters) >FitnessBrowser__Burk376:H281DRAFT_01038 Length = 703 Score = 651 bits (1680), Expect = 0.0 Identities = 334/663 (50%), Positives = 448/663 (67%), Gaps = 2/663 (0%) Query: 45 VKPLYTKKDVEDLPYADTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKA 104 +K +YT+ D+E + + D++PG AP++RGP A+MY +PWTIRQYAG++ A ++N +R A Sbjct: 14 LKRVYTRADIEGIAHIDSMPGEAPFVRGPFASMYTQKPWTIRQYAGYAQASDTNLAFRTA 73 Query: 105 LAAGGQGVSVAFDLATHRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSM 164 LA G QG+SVAFDL T RGYDSD+P V DVG GVAID+VEDM LF+ I LD++SVSM Sbjct: 74 LAEGAQGLSVAFDLPTQRGYDSDDPAVSADVGMTGVAIDTVEDMTRLFEDIALDRVSVSM 133 Query: 165 TMNGAVLPILAGYIVAAEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIF 224 TMNGAVLP+LA +IVAAEE GV QL GTIQNDILKEFMVRNT I+ P+PS++I +D+ Sbjct: 134 TMNGAVLPVLAAFIVAAEESGVGASQLRGTIQNDILKEFMVRNTSIFAPEPSLRIAADVV 193 Query: 225 GYTAQHMPKFNSISISGYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLS 284 Y +++P+FN++S+SGYH QEAGA+ +ELA T+A+ +Y+ G+ D R+S Sbjct: 194 EYLGKNVPRFNALSVSGYHFQEAGADPVLELALTMANARKYITALAGRGMQADDVCQRMS 253 Query: 285 FFWAVGMNFYLEIAKMRAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNV 344 FF+ VGM+FY+EIAK+RA R+LW I S S ++ LR H QTSGWSLT Q P NNV Sbjct: 254 FFFGVGMDFYVEIAKLRAARILWADIASASGATSDRARALRMHCQTSGWSLTAQKPMNNV 313 Query: 345 VRTTIEAMAAVFGGTQSLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAG 404 VRTT+EA+AAVFGGTQSLHTN DEA++LP ++R+AR+TQL++Q ET +C+VVDPWAG Sbjct: 314 VRTTVEALAAVFGGTQSLHTNGYDEALSLPCADASRLARDTQLVLQHETGVCDVVDPWAG 373 Query: 405 SYMMEKLTQDMADKAWSIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIV 464 SYMMEK T ++ KA +++ EIE GG+ VESGW + Q+ A + QA I+S K +V Sbjct: 374 SYMMEKFTAEICQKALTVMAEIERRGGVVDVVESGWVRDQIHRSALNIQAEIESRKRTVV 433 Query: 465 GVNKYKL-AKEDQIDILDIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEG 523 GVN + ED + +D VR Q RL I+A RD V+ LDALT+ A +G Sbjct: 434 GVNDFMTGCDEDLGEPQTVDGRRVRVLQTQRLAHIKARRDPTRVRNTLDALTRAARGRDG 493 Query: 524 NLLDLSVKAIRLRATVGEVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAK 583 NLL+L+V +R RATVGE + ALE V+ R++ + YG +E + W+ +A Sbjct: 494 NLLELTVACMRARATVGECTQALEAVWPRYQIGLPLLRDHYGANLESDKDWQDTCRAVAD 553 Query: 584 FAEEEGRRPRIMIAKLGQDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDV 643 + GR PR++IAKLGQDGHDRGA+++A A +D GF + G +F +P + + A V Sbjct: 554 ATKRLGRAPRVLIAKLGQDGHDRGARIIAAALSDAGFAVFTGSMFASPSDTVQLAEGERV 613 Query: 644 HAIGVSSLAAGHKTLLPALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGT 703 IGVSSLA L+ AL + L +G I + GG+I L +G A F GT Sbjct: 614 DVIGVSSLAGAQNDLITALHDQLTVRGL-RIPIVVGGIIDQASQLVLRRSGVAACFPAGT 672 Query: 704 RIE 706 I+ Sbjct: 673 PIK 675 Lambda K H 0.317 0.132 0.380 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: 1122 Number of extensions: 39 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: 721 Length of database: 703 Length adjustment: 39 Effective length of query: 682 Effective length of database: 664 Effective search space: 452848 Effective search space used: 452848 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 (21.6 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