Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_092481598.1 BM299_RS01005 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_900115975.1:WP_092481598.1 Length = 588 Score = 423 bits (1088), Expect = e-123 Identities = 232/569 (40%), Positives = 352/569 (61%), Gaps = 17/569 (2%) Query: 4 FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKF----MTDDGFEIKR--IYTPADLGE 57 ++ E L+K+ E W+E+ ++K E +E + T G E+ R +YTP + Sbjct: 28 YNPEALEKLSHEFNVWKESILRK------EDRENWHVIPRTVLGSELPRELLYTPLSVA- 80 Query: 58 DWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLS 117 D +YME +GF G+ PF RG++A MYRGR +T RQ G+ E++N R K+LL G TGL+ Sbjct: 81 DVDYMEDIGFSGQEPFARGIHANMYRGRTFTQRQLVGFGGPEDTNARMKFLLQHGATGLN 140 Query: 118 VAFDLPTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTIN--STAA 175 + FD+PT YDSD P++ G+VG G ID D +LFDGI + K +TS+ + S A Sbjct: 141 LLFDMPTIQMYDSDDPMSRGQVGSCGACIDCANDWELLFDGIDIGKETTSIVTHYPSNTA 200 Query: 176 NLLAMYILVAEEQGVSQEKLRGTVQNDI-LKEYIARGTYIFPPQPSMRLTTDIIMYCAEN 234 L MY+++AE +G S ++LRG+VQND+ L+E + + PP+ R+ D I + ++ Sbjct: 201 ILFPMYLVLAERRGTSWDQLRGSVQNDMTLEELVRNASEYIPPRDCFRIECDNIEFIRQH 260 Query: 235 VPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAH 294 VP+WN I+++GY++RE G + V E+A LA +E + +I RG DVD RL+FF++ Sbjct: 261 VPRWNFITLNGYNLREFGTSGVTEMAVALAHAMEILDEMIRRGHDVDWIGERLAFFWSPA 320 Query: 295 NNFLEEIAKFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAI 354 +F EEI + RA RRLW IMK + AK PRSM +R H QT+G +L ++P NNI+R A Sbjct: 321 MDFFEEICRLRAVRRLWYKIMKYKYQAKKPRSMWMRCHVQTSGISLVREEPLNNIIRSAY 380 Query: 355 QALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIE 414 +ALAAVLGG QSLH +SYDEA ++P+E++ ++LR QQI+ E+GV VDPLGG++YIE Sbjct: 381 EALAAVLGGAQSLHVDSYDEAYAIPSEEASLLSLRNQQILENETGVTAVVDPLGGSFYIE 440 Query: 415 WLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAF 474 LT+ I ++ L I +I++ GG + A+ G++ ++I Y K IE G IV N Sbjct: 441 ALTNEIEQKILSEIAEIEEQGGYVEAVSSGFLLQKIYHYFYNEHKRIENGAIKIVAHNWQ 500 Query: 475 VTDEPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYII 534 + + E + ++QI RLK+ +++RD++KV+ AL L +A K+ N++PY + Sbjct: 501 KSSRGEDFEAFRYPEDAEQRQIRRLKEFKAQRDSQKVESALRALEDAC-KKGVNVVPYTL 559 Query: 535 EAHRHLATLQEVTDVLREIWGEYRAPLIF 563 E R T+ E V ++ +G + P F Sbjct: 560 ECARAGCTVGEQWKVFKKAFGLWSKPSFF 588 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: 748 Number of extensions: 33 Number of successful extensions: 3 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: 588 Length adjustment: 36 Effective length of query: 527 Effective length of database: 552 Effective search space: 290904 Effective search space used: 290904 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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