Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate Dsui_1105 Dsui_1105 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__PS:Dsui_1105 Length = 1093 Score = 310 bits (795), Expect = 1e-88 Identities = 219/596 (36%), Positives = 322/596 (54%), Gaps = 50/596 (8%) Query: 5 DKEVLKKIKEEEKRWEETT--------VKKFLEKAPERKEKFMTDDGFEIKRIYTP--AD 54 + E+ K K+ W +T V K +K K + G +IK++ P D Sbjct: 503 ESELDAKAKKLLDMWPDTVKAYSGDEYVVKIRDKEIRTKLVSESLSGTKIKKVVLPRFTD 562 Query: 55 LGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQT 114 GE ++ K PG +P+T GV+A G T R +AG A +N+R+K + S+G Sbjct: 563 DGETLRFLMKENVPGSFPYTAGVFAFKREGEDPT-RMFAGEGDAFRTNRRFKKV-SEGMP 620 Query: 115 G--LSVAFDLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMT 169 LS AFD T G D D P G++G GV+I +L DM++L+ G L S SMT Sbjct: 621 AHRLSTAFDSVTLYGCDPDVRPDIYGKIGNSGVSIATLDDMKVLYSGFDLVCPTTSVSMT 680 Query: 170 INSTAANLLAMYILVAEEQGVSQ--------------EKLR--------GTVQNDILKEY 207 IN A +LA + A +Q + + EK+R GTVQ DILKE Sbjct: 681 INGPAPIILACFFNTAIDQQLDKFRADNGREPTEDEAEKIREWVLASVRGTVQADILKED 740 Query: 208 IARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGANAVQEVAFTLADG 266 + T IF + ++++ DI + N V + +SISGYHI EAGAN + ++AFTLA+G Sbjct: 741 QGQNTCIFSTEFALKMMGDIQEFFVHNQVQNFYSVSISGYHIAEAGANPISQLAFTLANG 800 Query: 267 IEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFNAKNPR 325 YV++ + RGM +D FAP LSFFF+ N E + R ARR+WA MK + A N R Sbjct: 801 FTYVESYLARGMHIDDFAPNLSFFFS--NGMDPEYSVIGRVARRIWAVAMKNKYGA-NER 857 Query: 326 SMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVR 385 S L++H QT+G +L AQ+ + N +R +QAL A+ SLHTN+YDEA++ PTE+SVR Sbjct: 858 SQKLKYHIQTSGRSLHAQEMDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTEESVR 917 Query: 386 IALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGY 445 A+ Q II E GV +P GA+ I+ LTD + E LK E I GG++ A+E GY Sbjct: 918 RAMAIQLIINREWGVAKNENPNQGAFIIDELTDLVEEAVLKEFEAIASRGGVLGAMETGY 977 Query: 446 VQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDE---PIEVEILKVDPSIREKQIERLKKL 502 + +I E + Y+ + +G I+GVN F+ + +E+E+ + ++ QI RLK Sbjct: 978 QRGKIQEESLYYEHKKHDGSYPIIGVNTFLNPKGSAQVEIELARSTEEEKQSQIARLKDF 1037 Query: 503 RSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558 +R+ K L KL+ E+ N+ ++EA R + +L ++T L E+ G+YR Sbjct: 1038 H-QRNADKAPAMLAKLKQTV-IENGNVFAVLVEAVR-VCSLGQITGALYEVGGQYR 1090 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: 1212 Number of extensions: 66 Number of successful extensions: 7 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: 563 Length of database: 1093 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1052 Effective search space: 549144 Effective search space used: 549144 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