GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mcm-large in Pedobacter sp. GW460-11-11-14-LB5

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate CA265_RS14780 CA265_RS14780 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS14780 CA265_RS14780
            methylmalonyl-CoA mutase
          Length = 1129

 Score =  228 bits (580), Expect = 1e-63
 Identities = 142/370 (38%), Positives = 219/370 (59%), Gaps = 12/370 (3%)

Query: 195  LRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCA-ENVPKWNPISISGYHIREAGA 253
            +RGTVQ DILKE  A+ T IF  + ++R+  DI  Y   E V  +  +SISGYHI EAGA
Sbjct: 763  VRGTVQADILKEDQAQNTCIFSTEFALRMMGDIQKYFIDEKVRNFYSVSISGYHIAEAGA 822

Query: 254  NAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWA 312
            N + ++AFTL++G  +V+  + RGM +D FAP LSFFF+  N    E A   R ARR+WA
Sbjct: 823  NPISQLAFTLSNGFTFVEYYLSRGMHIDDFAPNLSFFFS--NGIDPEYAVIGRVARRIWA 880

Query: 313  YIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSY 372
              +K  +   N RS  L++H QT+G +L AQ+ + N +R  +QAL A+     SLHTN+Y
Sbjct: 881  KAIKNKYKG-NDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAY 939

Query: 373  DEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQ 432
            DEA++ PTE+SVR A+  Q II  E G+    +PL GA+ IE LTD + +  L   ++I 
Sbjct: 940  DEAITTPTEESVRRAMAIQLIINRELGLAKNENPLQGAFIIEELTDLVEDAVLAEFKRIN 999

Query: 433  KMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP----IEVEILKVD 488
              GG++ A+E  Y + +I E +  Y+     G+  IVGVN F+        +  E+++  
Sbjct: 1000 DRGGVLGAMETMYQRGKIQEESLYYETLKHTGEYPIVGVNTFLNKNGSPTIVPGEVIRAT 1059

Query: 489  PSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTD 548
               ++ QI  L+K + +R+  +  + L +L+ +A   D N+   ++E  + + +L +++ 
Sbjct: 1060 EDEKQYQISALQKFQ-DRNADRAVDLLKQLQKSAIAGD-NIFEQLMEVCK-ICSLGQISK 1116

Query: 549  VLREIWGEYR 558
             L E+ G+YR
Sbjct: 1117 ALYEVGGQYR 1126



 Score = 75.5 bits (184), Expect = 1e-17
 Identities = 67/226 (29%), Positives = 108/226 (47%), Gaps = 16/226 (7%)

Query: 6   KEVLKKIKEEEKRW-EETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPA--DLGEDWNYM 62
           K +L++  + ++ + EE  + K  +K  ++   + +     I ++  P   D G+   ++
Sbjct: 502 KRLLRQWPDTKRAYKEEFFIYKVRDKEIKQPLFYESLSKLNIPKVSLPRYEDWGDILRWL 561

Query: 63  EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYL-LSQGQTGLSVAFD 121
                PGE+P+  GV+     G   T R +AG    E +NKR+ Y+ L Q    LS AFD
Sbjct: 562 LTENLPGEFPYAAGVFPLKREGEDPT-RMFAGEGGPERTNKRFHYVSLGQPAHRLSTAFD 620

Query: 122 LPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTAANLL 178
             T  G D    P   G++G  GV I +L D + L+ G  L     S SMTIN  A  LL
Sbjct: 621 SVTLYGEDPHIRPDIYGKIGNSGVCIATLDDAKKLYSGFDLCAPSTSVSMTINGPAPMLL 680

Query: 179 AMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFP----PQPS 220
             ++  A    + Q+  +  ++ND+ KE  A+   I+     P+PS
Sbjct: 681 GFFMNAA----IDQQCEKYIIENDLTKEVEAKIDAIYQAKNIPRPS 722


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: 1304
Number of extensions: 67
Number of successful extensions: 6
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: 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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