Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate RR42_RS01600 RR42_RS01600 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__Cup4G11:RR42_RS01600 Length = 1102 Score = 291 bits (746), Expect = 7e-83 Identities = 209/587 (35%), Positives = 319/587 (54%), Gaps = 58/587 (9%) Query: 7 EVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPA--DLGEDWNYMEK 64 E + KI+++E R TT T G ++++ P D GE ++ + Sbjct: 536 EYVVKIRDKEIRTTLTTT---------------TLSGTTVRKVVLPRFEDDGEVLKWLLR 580 Query: 65 LGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTG--LSVAFDL 122 PG +P+T GV+A T R +AG A +N+R+K L+S+G LS AFD Sbjct: 581 ENVPGSFPYTAGVFAFKRENEDPT-RMFAGEGDAFRTNRRFK-LVSEGMDAKRLSTAFDS 638 Query: 123 PTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTS--MTINSTAANLLA 179 T G D P G+VG GV+I +L DM++L+DG L STS MTIN A +LA Sbjct: 639 VTLYGEDPHTRPDIYGKVGNSGVSIATLDDMKVLYDGFDLTSPSTSVSMTINGPAPTILA 698 Query: 180 MYILVA------------------EEQGVSQ----EKLRGTVQNDILKEYIARGTYIFPP 217 M++ A +EQG + + +RGTVQ DILKE + T IF Sbjct: 699 MFMNTAIDQQFDKFRADNDREPTVDEQGKIRAWVLQNVRGTVQADILKEDQGQNTCIFST 758 Query: 218 QPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIER 276 + S+++ DI Y + V + +SISGYHI EAGAN + ++AFTL++G YV+A + R Sbjct: 759 EFSLKVMGDIQAYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFTLSNGFTYVEAYLAR 818 Query: 277 GMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFNAKNPRSMMLRFHTQT 335 GM +D FAP LSFFF+ N E + R ARR+WA +++ + A N RS L++H QT Sbjct: 819 GMHIDDFAPNLSFFFS--NGMDPEYSVLGRVARRIWAVTLRDKYGA-NERSQKLKYHIQT 875 Query: 336 AGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIA 395 +G +L AQ+ + N +R +QAL A+ SLHTN+YDEA++ PT +SVR AL Q II Sbjct: 876 SGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTGESVRRALAIQLIIN 935 Query: 396 YESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAY 455 E GV +P G++ I+ LTD + + ++ E+I + GG++ A+E GY + +I + + Sbjct: 936 REWGVARCENPNQGSFLIDELTDLVEDAVMQEFERIAERGGVLGAMETGYQRGKIQDESL 995 Query: 456 KYQKEIEEGKRIIVGVNAFVTDE----PIEVEILKVDPSIREKQIERLKKLRSERDNKKV 511 Y++ +G I+GVN F + P +E+ + ++ Q+ RL + R Sbjct: 996 YYEQRKHDGTLPIIGVNTFRNPDGDAAPPSLELARSSEEEKQGQLARLADFHA-RHADAA 1054 Query: 512 QEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558 L +LR A ++ N+ +++A R + +L +VT L E+ G+YR Sbjct: 1055 PAMLQRLRQAV-IDNGNVFAVLMDAVR-VCSLGQVTHALFEVGGQYR 1099 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: 8 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: 1102 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1061 Effective search space: 553842 Effective search space used: 553842 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