GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Burkholderia phytofirmans PsJN

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate BPHYT_RS02085 BPHYT_RS02085 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>FitnessBrowser__BFirm:BPHYT_RS02085
          Length = 1298

 Score =  308 bits (790), Expect = 7e-88
 Identities = 205/554 (37%), Positives = 311/554 (56%), Gaps = 43/554 (7%)

Query: 40   TDDGFEIKRIYTP--ADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYAT 97
            T  G E++++  P  AD GE   ++     PG +PFT GV+         T R +AG   
Sbjct: 750  TLSGSEVRKVSLPKFADHGEILRWLMLDNLPGYFPFTAGVFPFRRENEDPT-RMFAGEGD 808

Query: 98   AEESNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRI 154
             + +N+R+K LLS+G     LS AFD  T  G + D  P   G+VG  GV++ +L DM+ 
Sbjct: 809  PQRTNRRFK-LLSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMKT 867

Query: 155  LFDGIPL--DKVSTSMTINSTAANLLAMYILVAEEQGVSQ-------------------- 192
            L+DG  L   + S SMTIN  A  +LAM+  VA +Q +++                    
Sbjct: 868  LYDGFDLCAPETSVSMTINGPAPTILAMFFNVAIDQQIARMTQQQGRPLTHDELSATRRA 927

Query: 193  --EKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIR 249
              E +RGTVQ DILKE   + T IF  + S+++  DI  Y  E+ V  +  +SISGYHI 
Sbjct: 928  ALENVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHGVRNFYSVSISGYHIA 987

Query: 250  EAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAAR 308
            EAGAN + ++A+TLA+G  YV+A + RGM +D FAP LSFFF+  N    E     R AR
Sbjct: 988  EAGANPISQLAYTLANGFTYVEAYLARGMSIDDFAPNLSFFFS--NGMDPEYTVLGRVAR 1045

Query: 309  RLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLH 368
            R+WA  M+E + A N RS  L++H QT+G +L AQ+ + N +R  +QAL A+     SLH
Sbjct: 1046 RIWAVAMRERYGA-NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLH 1104

Query: 369  TNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYI 428
            TN++DEA++ PTE SVR A+  Q II  E G+    +P  G++ IE LTD + E  L   
Sbjct: 1105 TNAFDEAITTPTEDSVRRAVAIQLIINREWGLAKNQNPNQGSFVIEELTDLVEEAVLAEF 1164

Query: 429  EKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIE----VEI 484
            +++ + GG++ A+E GY +  I + +  Y+    +G   IVGVN F++  P E    + +
Sbjct: 1165 DRLTERGGVLGAMETGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFLSAHPHEAPQPIAL 1224

Query: 485  LKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQ 544
             +     ++ Q++RL+  +S+        AL++L+ A   +DEN+   +++  R + +L 
Sbjct: 1225 ARSTDDEKQSQLQRLRAFQSQH-RDAAPAALERLKRAV-IDDENVFAVLMDVVR-VCSLG 1281

Query: 545  EVTDVLREIWGEYR 558
            ++T  L E+ G+YR
Sbjct: 1282 QITHALFEVGGQYR 1295


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: 1344
Number of extensions: 61
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: 1298
Length adjustment: 42
Effective length of query: 521
Effective length of database: 1256
Effective search space:   654376
Effective search space used:   654376
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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