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::Q84FZ1 (721 letters) >FitnessBrowser__Cola:Echvi_4683 Length = 685 Score = 872 bits (2252), Expect = 0.0 Identities = 431/670 (64%), Positives = 527/670 (78%), Gaps = 2/670 (0%) Query: 40 FYGPEDREGCEGIDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAA 99 F DR + + G+ P+LRGPY MY+T+PWT+RQYAGFSTAE SNAFY++NL A Sbjct: 14 FMEAADRPRPDHVRYAAGIAPFLRGPYSTMYLTRPWTLRQYAGFSTAEASNAFYKKNLEA 73 Query: 100 GQKGLSVAFDLATHRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMN 159 GQKGLSVAFDLATHRGYDSDHPRV GDVG AGVAIDS+ M+ LF GIPLD+M+VSMTMN Sbjct: 74 GQKGLSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVLGMKLLFDGIPLDKMSVSMTMN 133 Query: 160 GAVLPGVALYIVAAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYT 219 GAV+P +A YIVAAEEQGVP ++L GTIQNDILKEFMVRNTYIYPP+ S+RII+DIF +T Sbjct: 134 GAVIPVMAFYIVAAEEQGVPLDQLKGTIQNDILKEFMVRNTYIYPPEPSLRIIADIFAFT 193 Query: 220 SKNMPKFNSISISGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFW 279 +KNMP FNSISISGYHM EAGAT +LELAYTLADG+EY++ GL AGL ID FAPRLSFFW Sbjct: 194 AKNMPAFNSISISGYHMLEAGATPELELAYTLADGLEYVRTGLKAGLAIDDFAPRLSFFW 253 Query: 280 AIGMNFFMEIAKMRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRT 339 +GM+ F EIAK+RA RL+WAKL+KEF P KSL LR H QTSGWSLT QD FNNV RT Sbjct: 254 GVGMDHFTEIAKLRAGRLLWAKLMKEFRPTHPKSLKLRAHCQTSGWSLTEQDAFNNVART 313 Query: 340 CIEAMAATQGGTQSLHTNALDEALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYY 399 IEA+AA G TQSLHTNA DEA ALPTDFSA IARNTQ+ L++E G +++DPWGGS Sbjct: 314 TIEALAAVMGHTQSLHTNAFDEAFALPTDFSASIARNTQVILREEYGLRKVVDPWGGSVL 373 Query: 400 VERLTRDIAARAWEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGIN 459 +E LT D+ +AW H++EVE +GGMAKAIEAG+PK IEEAAAR QA++D G++ +VG+N Sbjct: 374 LEELTEDLVKKAWAHLQEVEKMGGMAKAIEAGLPKQMIEEAAARRQAKVDQGKEIVVGVN 433 Query: 460 KYKPDDEMKIDLLRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTKAA-DGEGNLLE 518 ++ D+E D+L VDN V +Q +L +L+ +R+ A V +L A+T+AA GEGNLLE Sbjct: 434 RFLVDEEEDFDILEVDNEAVLKQQQARLSQLKNDRDAAAVARSLEAITQAAKSGEGNLLE 493 Query: 519 LAVNAARAKATVGEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEE 578 L+V AAR +AT+GEIS A+EK +GRHRA+ + +SGVY E G + ++ L FE+ Sbjct: 494 LSVEAARERATLGEISMAMEKVYGRHRAKNQVVSGVYSSEAGN-DELFKEALTLTARFEK 552 Query: 579 NDGRRPRILVAKMGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIV 638 +GRRPRIL+AKMGQDGHDRG KVIAS AD+GFDVDIGPLF TP+E A+QAVENDVH+V Sbjct: 553 LEGRRPRILIAKMGQDGHDRGAKVIASGMADMGFDVDIGPLFQTPEEVAKQAVENDVHLV 612 Query: 639 GVSSLAAGHLTLVPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIA 698 G SSLA GH L+P+L AL++ GR D+++V GGVIPP DY+ L G +F PGTV+ Sbjct: 613 GASSLAGGHKVLIPQLIIALEEMGRPDILVVAGGVIPPHDYEFLKEKGVLEVFGPGTVLT 672 Query: 699 EAAVNLLGEL 708 +AA+ ++ L Sbjct: 673 KAAIRIMSVL 682 Lambda K H 0.318 0.134 0.391 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: 1263 Number of extensions: 48 Number of successful extensions: 4 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: 685 Length adjustment: 39 Effective length of query: 682 Effective length of database: 646 Effective search space: 440572 Effective search space used: 440572 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