Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate Echvi_2441 Echvi_2441 Methylmalonyl-CoA mutase, N-terminal domain/subunit
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__Cola:Echvi_2441 Length = 1125 Score = 267 bits (682), Expect = 2e-75 Identities = 200/576 (34%), Positives = 291/576 (50%), Gaps = 85/576 (14%) Query: 59 WNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYL-LSQGQTGLS 117 W + E + PG++PFT GV+ G T R +AG E +N+R+ Y+ LS Sbjct: 556 WKFKENV--PGKFPFTAGVFPFKREGEDPT-RMFAGEGGPERTNRRFHYVSKDMPAKRLS 612 Query: 118 VAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTA 174 AFD T G D + P G++G GV I L DM+ L+ G L + S SMTIN A Sbjct: 613 TAFDSVTLYGEDPGYRPDIYGKIGNSGVNICCLDDMKKLYAGFDLADPRTSVSMTINGPA 672 Query: 175 ANLLAMYILVA--------------------------EEQGVSQEKLRGTV--------- 199 A + A ++ A E G+ + + +GTV Sbjct: 673 ATMTAFFMNTAIDQQCERYIYDKGSEGEVEAKLDEMYRENGLERPRYQGTVPEGNNGLGL 732 Query: 200 -------------------------------QNDILKEYIARGTYIFPPQPSMRLTTDII 228 Q DILKE A+ T IF + S+RL D+ Sbjct: 733 LLLGVTGDQVLPKEVYESIKADTLTKVRGTVQADILKEDQAQNTCIFSTEFSLRLMGDVQ 792 Query: 229 MY-CAENVPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRL 287 Y + V + +SISGYHI EAGAN + ++A TL++G YV+ + RGMDV+ FAP L Sbjct: 793 EYFIDQGVRNFYSVSISGYHIAEAGANPITQLALTLSNGFTYVEYYVSRGMDVNAFAPNL 852 Query: 288 SFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPE 346 SFFF+ N E A R ARR+WA MK + A N RS ML++H QT+G +L AQ+ + Sbjct: 853 SFFFS--NGIDPEYAVIGRVARRIWAKAMKLKYGA-NERSQMLKYHIQTSGRSLHAQEID 909 Query: 347 NNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDP 406 N +R +QAL A+ SLHTN+YDEA++ PTE SVR A+ Q II E G+ +P Sbjct: 910 FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEASVRRAMAIQLIINKELGLAKNENP 969 Query: 407 LGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKR 466 L GA+ IE LTD + E E+I + GG++ A+E Y + +I E + Y+ G Sbjct: 970 LQGAFIIEELTDLVEEAVYAEFERITERGGVLGAMETMYQRGKIQEESLHYETLKHAGTY 1029 Query: 467 IIVGVNAFVTDEPIEV----EILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAA 522 I+GVN F++ E+++ +E QI+ L+ L + + + V E L+ L+ AA Sbjct: 1030 PIIGVNTFLSSAGSPTITPGEVIRATQEEKEMQIKGLENLHRKYEFQSV-ELLNDLKEAA 1088 Query: 523 EKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558 +ENL ++EA + +L ++T L E+ G++R Sbjct: 1089 -VTNENLFSQLMEAVK-CCSLGQITHALYEVGGQFR 1122 Lambda K H 0.318 0.134 0.388 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: 1344 Number of extensions: 74 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 563 Length of database: 1125 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1084 Effective search space: 565848 Effective search space used: 565848 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 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