Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_013450693.1 CALNI_RS02840 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_000183405.1:WP_013450693.1 Length = 716 Score = 884 bits (2284), Expect = 0.0 Identities = 444/687 (64%), Positives = 548/687 (79%), Gaps = 6/687 (0%) Query: 38 WETAEQIPVGTLFNEDVYKDMDW-LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAK 96 W TAE V L+ + K++ + +DTY G+PPFV GP ATMYA +PWT+RQYAGFSTA+ Sbjct: 30 WHTAEGFDVKPLYTAEDLKNLTFDIDTYPGLPPFVRGPMATMYAGKPWTVRQYAGFSTAE 89 Query: 97 ESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGI 156 ESNAFY+RNLAAGQ+GLSVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF GI Sbjct: 90 ESNAFYKRNLAAGQQGLSVAFDLATHRGYDSDHPRVIGDVGKAGVAIDSVEDMKILFDGI 149 Query: 157 PLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQP 216 PLD++SVSMTMNGAV+P++A Y+V AEEQGV ++L+GTIQNDILKEFMVRNTYIYPP+P Sbjct: 150 PLDKVSVSMTMNGAVIPVMAFYIVAAEEQGVSQDKLSGTIQNDILKEFMVRNTYIYPPEP 209 Query: 217 SMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLN 276 SMRI+++I YTS MPK+NSISISGYH+QEAGA + +E+A+TLADG++Y+R S GL+ Sbjct: 210 SMRIVADIIEYTSKYMPKFNSISISGYHIQEAGANSALELAFTLADGLEYVRTALSRGLD 269 Query: 277 VDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSL 336 +D+FAPRLSFF+ IGMNFFME+AKLRAAR LWAKL+ QF PK+PKSM+LRTH QTSGWSL Sbjct: 270 IDKFAPRLSFFFAIGMNFFMEIAKLRAARYLWAKLISQFNPKDPKSMALRTHCQTSGWSL 329 Query: 337 TAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGT 396 TAQD YNNV+RT IEA+AA G TQSLHTN+LDEA+ALPTDFSARIARNTQL +Q+E+ Sbjct: 330 TAQDPYNNVIRTTIEALAAVLGGTQSLHTNALDEALALPTDFSARIARNTQLIIQEETNI 389 Query: 397 TRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQAR 456 VIDP GS YVE LT +L ++A I EVE +GGM KAIE G+PK++IEE+AA+ QAR Sbjct: 390 CNVIDPLGGSYYVENLTNELIKEAEKIIAEVEALGGMTKAIETGMPKLKIEESAAKKQAR 449 Query: 457 IDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKIT 516 IDSG ++GVNKY+LE E P+DVL +DN+ V Q KL +++ +RD + VK AL+KIT Sbjct: 450 IDSGLDVIVGVNKYKLEKEDPIDVLMIDNTAVRNRQIQKLNEIKGKRDNKAVKEALEKIT 509 Query: 517 WAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKN 576 AA + D+NLL+ ++A R AT+GE+SDA+E VFGRY A+IR +G Y Sbjct: 510 EAA-----RSNDKNLLEYAVNAARLRATLGEISDAMEAVFGRYKAEIRLQTGTYGNAYGK 564 Query: 577 TPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQT 636 +EE RELV+EFE+ EGRRPRIL+ KMGQDGHDRG KV+ATA AD+GFDVDVGP+FQT Sbjct: 565 KDMIEEVRELVKEFEEVEGRRPRILMVKMGQDGHDRGVKVVATALADMGFDVDVGPMFQT 624 Query: 637 PEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDEL 696 PEE A+ A+E DVH VGVS+LA GH TLVPAL +EL K DI++ VGGVIP QD++ L Sbjct: 625 PEEAAKMAIENDVHAVGVSTLAAGHNTLVPALVEELKKNDGDDIVVFVGGVIPPQDYEFL 684 Query: 697 RKDGAVEIYTPGTVIPESAISLVKKLR 723 K GA ++ PGT I ESA +++ +R Sbjct: 685 YKSGASAVFGPGTNIVESAKKILECIR 711 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: 1348 Number of extensions: 45 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: 716 Length adjustment: 40 Effective length of query: 688 Effective length of database: 676 Effective search space: 465088 Effective search space used: 465088 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