GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Chryseobacterium arthrosphaerae CC-VM-7

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_065399519.1 BBI00_RS15060 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_001684965.1:WP_065399519.1
          Length = 1115

 Score =  238 bits (606), Expect = 1e-66
 Identities = 150/380 (39%), Positives = 230/380 (60%), Gaps = 12/380 (3%)

Query: 185  AEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMY-CAENVPKWNPISI 243
            AE +  +   +RGTVQ DILKE  A+ T IF  + ++RL  D+  Y   E V  +  +SI
Sbjct: 739  AEIKAKTIATVRGTVQADILKEDQAQNTCIFSTEFALRLMGDVQEYFIKEKVRNFYSVSI 798

Query: 244  SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303
            SGYHI EAGAN V ++AFTLA+G  YV+  + RGMD++ FAP LSFFF+  N    E + 
Sbjct: 799  SGYHIAEAGANPVSQLAFTLANGFTYVEYYLSRGMDINDFAPNLSFFFS--NGIDPEYSV 856

Query: 304  F-RAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLG 362
              R ARR+WA  MK  + A + RS ML++H QT+G +L AQ+ + N +R  +QAL A+  
Sbjct: 857  IGRVARRIWAKAMKLKYGA-DERSQMLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYD 915

Query: 363  GTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYE 422
               SLHTN+YDEA++ PTE+SVR A+  Q II  E G+    +PL G++ IE LTD + E
Sbjct: 916  NCNSLHTNAYDEAITTPTEQSVRRAMAIQLIINKELGLAKNENPLQGSFIIEELTDLVEE 975

Query: 423  EALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFV----TDE 478
                  ++I + GG++ A+E  Y + +I E +  Y+     G+  I+GVN F+    +  
Sbjct: 976  AVYTEFDRITERGGVLGAMETMYQRSKIQEESMHYEWLKHTGEYPIIGVNTFLGKDGSPT 1035

Query: 479  PIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHR 538
             +  E+++     ++ QIE L   +   ++K  +EAL  L++AA  + +NL   +++A +
Sbjct: 1036 VLPGEVIRSTEEEKQAQIEFLHNFQKANESKS-EEALRTLQHAAINQ-QNLFEVMMDAVK 1093

Query: 539  HLATLQEVTDVLREIWGEYR 558
            +  +L ++T+ L E+ G+YR
Sbjct: 1094 Y-CSLGQITNALFEVGGKYR 1112



 Score = 67.8 bits (164), Expect = 2e-15
 Identities = 50/138 (36%), Positives = 70/138 (50%), Gaps = 7/138 (5%)

Query: 59  WNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTG-LS 117
           W   E L  PG +P+T G+Y     G   T R +AG    E +N+R+ Y+ ++     LS
Sbjct: 546 WKGQENL--PGSFPYTAGIYPFKRTGEDPT-RMFAGEGGPERTNRRFHYVSAEMPAKRLS 602

Query: 118 VAFDLPTQLGYDSDHPL-AEGEVGKVGVAIDSLWDMRILFDGIPLDKV--STSMTINSTA 174
            AFD  T  G D   P    G++G  GV+I +L D + L+ G  L     S SMTIN  A
Sbjct: 603 TAFDSVTLYGQDPALPPDIYGKIGNAGVSIATLDDAKKLYSGFDLVNALTSVSMTINGPA 662

Query: 175 ANLLAMYILVAEEQGVSQ 192
             LLA ++  A +Q V +
Sbjct: 663 PMLLAFFMNAAIDQNVEK 680


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: 1318
Number of extensions: 64
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 563
Length of database: 1115
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1074
Effective search space:   560628
Effective search space used:   560628
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.

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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