Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Echvi_4683 Echvi_4683 Methylmalonyl-CoA mutase, N-terminal domain/subunit
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Cola:Echvi_4683 Length = 685 Score = 865 bits (2234), Expect = 0.0 Identities = 419/658 (63%), Positives = 526/658 (79%), Gaps = 5/658 (0%) Query: 65 AGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRG 124 AGI PF+ GPY+TMY RPWT+RQYAGFSTA+ SNAFY++NL AGQKGLSVAFDL THRG Sbjct: 30 AGIAPFLRGPYSTMYLTRPWTLRQYAGFSTAEASNAFYKKNLEAGQKGLSVAFDLATHRG 89 Query: 125 YDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEE 184 YDSD+PRV GDVG AGVAIDS+ M+ LF GIPLD+MSVSMTMNGAV+P++A Y+V AEE Sbjct: 90 YDSDHPRVQGDVGKAGVAIDSVLGMKLLFDGIPLDKMSVSMTMNGAVIPVMAFYIVAAEE 149 Query: 185 QGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYH 244 QGV +QL GTIQNDILKEFMVRNTYIYPP+PS+RII++IFA+T+ NMP +NSISISGYH Sbjct: 150 QGVPLDQLKGTIQNDILKEFMVRNTYIYPPEPSLRIIADIFAFTAKNMPAFNSISISGYH 209 Query: 245 MQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAA 304 M EAGAT ++E+AYTLADG++Y+R G GL +D FAPRLSFFWG+GM+ F E+AKLRA Sbjct: 210 MLEAGATPELELAYTLADGLEYVRTGLKAGLAIDDFAPRLSFFWGVGMDHFTEIAKLRAG 269 Query: 305 RMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLH 364 R+LWAKL+ +F P +PKS+ LR H QTSGWSLT QD +NNV RT IEA+AA GHTQSLH Sbjct: 270 RLLWAKLMKEFRPTHPKSLKLRAHCQTSGWSLTEQDAFNNVARTTIEALAAVMGHTQSLH 329 Query: 365 TNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHI 424 TN+ DEA ALPTDFSA IARNTQ+ L++E G +V+DPW GS +EELT DL +KAW H+ Sbjct: 330 TNAFDEAFALPTDFSASIARNTQVILREEYGLRKVVDPWGGSVLLEELTEDLVKKAWAHL 389 Query: 425 QEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVD 484 QEVEK+GGMAKAIE G+PK IEEAAAR QA++D G++ ++GVN++ ++ E D+L+VD Sbjct: 390 QEVEKMGGMAKAIEAGLPKQMIEEAAARRQAKVDQGKEIVVGVNRFLVDEEEDFDILEVD 449 Query: 485 NSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMAT 544 N VL +Q+A+L +L+ +RD V +L+ IT AA K + NLL+L ++A R AT Sbjct: 450 NEAVLKQQQARLSQLKNDRDAAAVARSLEAITQAA-----KSGEGNLLELSVEAARERAT 504 Query: 545 VGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAK 604 +GE+S A+EKV+GR+ A+ + +SGVYS E N +EA L FE+ EGRRPRIL+AK Sbjct: 505 LGEISMAMEKVYGRHRAKNQVVSGVYSSEAGNDELFKEALTLTARFEKLEGRRPRILIAK 564 Query: 605 MGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTL 664 MGQDGHDRG KVIA+ AD+GFDVD+GPLFQTPEE A+QAVE DVH+VG SSLAGGH L Sbjct: 565 MGQDGHDRGAKVIASGMADMGFDVDIGPLFQTPEEVAKQAVENDVHLVGASSLAGGHKVL 624 Query: 665 VPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722 +P L L+++GRPDIL+ GGVIP D++ L++ G +E++ PGTV+ ++AI ++ L Sbjct: 625 IPQLIIALEEMGRPDILVVAGGVIPPHDYEFLKEKGVLEVFGPGTVLTKAAIRIMSVL 682 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: 1286 Number of extensions: 50 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: 685 Length adjustment: 39 Effective length of query: 689 Effective length of database: 646 Effective search space: 445094 Effective search space used: 445094 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: 54 (25.4 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