Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_073036072.1 BUB04_RS00960 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_900129305.1:WP_073036072.1 Length = 559 Score = 714 bits (1843), Expect = 0.0 Identities = 352/555 (63%), Positives = 439/555 (79%), Gaps = 2/555 (0%) Query: 4 FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYME 63 +D + L++I+ ++ WE+TT+ K L K PERK F + G ++R+YTP D D +Y + Sbjct: 2 YDDKELERIRAGKENWEKTTLGKALSKFPERKPIFTSISGMPVERLYTPLDTA-DLDYEK 60 Query: 64 KLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLP 123 LG+PG+YPFTRGV TMYRGR WTMRQYAG+ A ESN RY+YLL QGQTGLSVAFDLP Sbjct: 61 DLGYPGQYPFTRGVQPTMYRGRFWTMRQYAGFGNARESNARYRYLLEQGQTGLSVAFDLP 120 Query: 124 TQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYIL 183 TQ GYDSDHPL+ GEVGKVGVAIDSL DM+ILFDGIPLD+V+TSMTIN+ A LLAMY+ Sbjct: 121 TQAGYDSDHPLSMGEVGKVGVAIDSLDDMKILFDGIPLDQVTTSMTINAPATVLLAMYLA 180 Query: 184 VAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISI 243 +AEEQGV +K+ GTVQNDILKE I RG YIFPP+PSMRLT D+I YC ++VP+WN ISI Sbjct: 181 IAEEQGVPFDKVGGTVQNDILKEIICRGQYIFPPKPSMRLTVDLIDYCFKHVPRWNTISI 240 Query: 244 SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303 SGYHIREAG+ A QE+AFT+ADGI YV+A ++RG+ VD FAPRLSFFF A N LEE+AK Sbjct: 241 SGYHIREAGSTAAQEMAFTIADGIAYVQACVDRGLAVDSFAPRLSFFFNAFTNVLEEVAK 300 Query: 304 FRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGG 363 FRA RR+WA IMKE F AK+PRSMM+R+H QT G TLTAQQP NNIVRVA+QA AA LGG Sbjct: 301 FRAGRRVWARIMKERFGAKDPRSMMMRYHVQTGGVTLTAQQPLNNIVRVALQAYAAALGG 360 Query: 364 TQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEE 423 QSLHTNSYDEAL LPT+++V +ALRTQQI+A ESG DT+DPL G+Y++E +TD I E Sbjct: 361 CQSLHTNSYDEALCLPTQEAVTVALRTQQIVAEESGATDTIDPLAGSYFVEAMTDKIEAE 420 Query: 424 ALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVE 483 +YI KI MGG + AIE+GY+QKEI ++AY++QKEIE G+R+ VG+N + +EP Sbjct: 421 IEEYIRKIDAMGGTLTAIEQGYIQKEIQDSAYRFQKEIESGERVYVGINKYTMEEPEPTN 480 Query: 484 ILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATL 543 +LKVD + E + E+LKKLR+ERD + + ALD+LR ++ DEN+MP +IEA + AT+ Sbjct: 481 LLKVDMKVGEIEAEKLKKLRAERDQAQWKAALDRLREVSQ-SDENVMPAVIEAVKARATI 539 Query: 544 QEVTDVLREIWGEYR 558 E+ DV R+++GEYR Sbjct: 540 GEICDVWRDVFGEYR 554 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: 915 Number of extensions: 37 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: 559 Length adjustment: 36 Effective length of query: 527 Effective length of database: 523 Effective search space: 275621 Effective search space used: 275621 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