Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_068167454.1 HTA01S_RS04855 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_001592305.1:WP_068167454.1 Length = 1129 Score = 291 bits (745), Expect = 1e-82 Identities = 210/605 (34%), Positives = 320/605 (52%), Gaps = 69/605 (11%) Query: 12 IKEEEKRWEETTVKKFLEKAPERKEKFMTDD--------------------GFEIKRIYT 51 + +E + ++ +K L + P+ ++ + D+ G I+++ Sbjct: 533 LAQERELAQDPAARKLLAQWPDMQKAYAGDEYVVKIRDKEIRTALTTKSLSGTSIRKVAL 592 Query: 52 PA--DLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLL 109 P D GE ++ PG YP+T G +A G T R +AG A +N+R+K LL Sbjct: 593 PQYEDHGEILKWLMLDNVPGSYPYTAGTFAFKREGEDPT-RMFAGEGDAFRTNRRFK-LL 650 Query: 110 SQGQTG--LSVAFDLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKV 164 S+G LS AFD T G D D P G+VG GV+I +L DM++L+ G L Sbjct: 651 SEGMPAKRLSTAFDSVTLYGNDPDPRPDIYGKVGNSGVSIATLDDMKVLYGGFDLCHPAT 710 Query: 165 STSMTINSTAANLLAMYILVAEEQGVSQEK----------------------LRGTVQND 202 S SMTIN A ++LAM++ A +Q V + K +RGTVQ D Sbjct: 711 SVSMTINGPAPSILAMFMNTAIDQNVEKFKADNGREPTDTEAQKIREWVLANVRGTVQAD 770 Query: 203 ILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGANAVQEVAF 261 ILKE + T IF + S+++ DI Y + V + +SISGYHI EAGAN + ++AF Sbjct: 771 ILKEDQGQNTCIFSTEFSLKVMGDIAEYFVHHDVRNFYSVSISGYHIAEAGANPISQLAF 830 Query: 262 TLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFN 320 TL++G +V+A + RGM +D FAP LSFFF+ N E R ARR+WA MKE + Sbjct: 831 TLSNGFTFVEAYLARGMHIDDFAPNLSFFFS--NGMDPEYTVLGRVARRIWAVAMKEKYG 888 Query: 321 AKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPT 380 A N RS L++H QT+G +L AQ+ + N +R +QAL A+ SLHTN++DEA++ PT Sbjct: 889 A-NERSQKLKYHIQTSGRSLHAQEIQFNDIRTTLQALIAIYDNCNSLHTNAFDEAITTPT 947 Query: 381 EKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRA 440 E SVR A+ Q II E G+ +P G++ IE LT+ + E L EKI + GG++ A Sbjct: 948 EDSVRRAMAIQLIINREWGLAKNENPNQGSFIIEQLTELVEEAVLAEFEKIAERGGVLGA 1007 Query: 441 IERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAF-------VTDEPIEVEILKVDPSIRE 493 +E GY + +I + + Y+ G+ I+GVN F V D ++E+ + ++ Sbjct: 1008 METGYQRGKIQDESMHYEMLKHTGEYPIIGVNTFRNPHGDAVMD---KLELARSTDEEKQ 1064 Query: 494 KQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREI 553 Q++RL + R + L +L+ A E+ N+ +++A R +L ++T L + Sbjct: 1065 SQLQRLAGFHA-RHAAEAPAMLQRLQQAV-IENRNVFEVLMDAVR-CCSLGQITGALFAV 1121 Query: 554 WGEYR 558 G+YR Sbjct: 1122 GGQYR 1126 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: 1249 Number of extensions: 64 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: 1129 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1088 Effective search space: 567936 Effective search space used: 567936 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 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