Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_072907423.1 BUB13_RS07410 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_900142125.1:WP_072907423.1 Length = 712 Score = 854 bits (2207), Expect = 0.0 Identities = 435/678 (64%), Positives = 521/678 (76%), Gaps = 5/678 (0%) Query: 38 WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKE 97 W+T E I V L+ + ++ DT G+ PFV GP ATMYA RPWT+RQYAGFSTA+E Sbjct: 30 WDTPEGISVKPLYTAADIEGLETADTMPGLAPFVRGPMATMYAGRPWTVRQYAGFSTAEE 89 Query: 98 SNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIP 157 SNAFY+RNLAAGQ+GLSVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF+ IP Sbjct: 90 SNAFYKRNLAAGQQGLSVAFDLATHRGYDSDHPRVVGDVGKAGVAIDSVEDMKILFSDIP 149 Query: 158 LDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPS 217 LD++SVSMTMNGAVLPI+A Y++ AEEQGV ++LAGTIQNDILKEFMVRNTYIYPP PS Sbjct: 150 LDKVSVSMTMNGAVLPIMANYIIAAEEQGVSEDKLAGTIQNDILKEFMVRNTYIYPPAPS 209 Query: 218 MRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNV 277 M+II +I YTS MPK+NSISISGYH+QEAGA +E+A+TLADG++Y+R + GL+V Sbjct: 210 MKIIGDIIEYTSQKMPKFNSISISGYHIQEAGANNALELAFTLADGLEYVRQAVAKGLDV 269 Query: 278 DQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLT 337 D FAPRLSFF+ IGMNFFME +KLRAAR LWAK++ QF PKNPKS LRTH QTSGWSLT Sbjct: 270 DAFAPRLSFFFAIGMNFFMEASKLRAARFLWAKMMKQFNPKNPKSSMLRTHCQTSGWSLT 329 Query: 338 AQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTT 397 QD YNNV+RT +EA+AA G TQSLHTN+LDEAIALPTD SARIARNTQL +Q+ESG Sbjct: 330 EQDPYNNVIRTTLEALAAVLGGTQSLHTNALDEAIALPTDHSARIARNTQLVIQEESGVC 389 Query: 398 RVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARI 457 V+DP GS YVE LT L +A + E+E++GGM KAIE G+PK+RIEE+AA+ QA I Sbjct: 390 NVVDPLGGSYYVESLTNSLIEEASKILDEIEELGGMTKAIESGMPKLRIEESAAKKQASI 449 Query: 458 DSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITW 517 DSGR ++GVNKY+L E ++VL VDN+ V Q A+L K+RA+RD + ALD IT Sbjct: 450 DSGRDVIVGVNKYKLAEEDEIEVLDVDNAAVRESQIARLNKMRADRDEAACQQALDAITA 509 Query: 518 AAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNT 577 A + NLL L + A R A+VGE+SDA+EKVFGR+ A+I+ +SG Y V Sbjct: 510 AC-----ESGAGNLLDLSVKAARLRASVGEISDAMEKVFGRHKAEIKLVSGAYGSVVNED 564 Query: 578 PEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTP 637 + E ++ ++ F EGRRPRIL+AKMGQDGHDRG KV+A+AYAD GFDVDVGPLFQTP Sbjct: 565 NDFNEVKKRIDAFAAKEGRRPRILVAKMGQDGHDRGAKVVASAYADAGFDVDVGPLFQTP 624 Query: 638 EETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELR 697 EE A+ AVE DVHVVGVSSLA GH TLVP L EL KLG DI + GGVIP QD+D L Sbjct: 625 EEAAKMAVENDVHVVGVSSLAAGHKTLVPQLVAELKKLGADDIAVVCGGVIPRQDYDALY 684 Query: 698 KDGAVEIYTPGTVIPESA 715 + GA +I+ PGT I SA Sbjct: 685 EAGAAKIFGPGTPITVSA 702 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: 1307 Number of extensions: 30 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 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