GapMind for catabolism of small carbon sources

 

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

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate CA265_RS25460 CA265_RS25460 methylmalonyl-CoA mutase

Query= SwissProt::O86028
         (712 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS25460 CA265_RS25460
           methylmalonyl-CoA mutase
          Length = 515

 Score =  488 bits (1256), Expect = e-142
 Identities = 253/515 (49%), Positives = 349/515 (67%), Gaps = 7/515 (1%)

Query: 28  TPEGIDVKPLYTSDDMSGIGHLNSLPGFEPFVRGPRATMYAGRPWTVRQYAGFSTAEASN 87
           T  GI++K LYT         +  LPG  PF RG +  MY GR WT+RQYAGFSTAE SN
Sbjct: 8   TTSGIEIKALYTKAKP-----MEELPGEFPFTRGIQKDMYRGRLWTMRQYAGFSTAEESN 62

Query: 88  AFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVEDMKILFDGIPLD 147
             Y   LA G  G+SVAFDL T  GYDSDH    G+VGK GVAIDS++D++ILFDGI L 
Sbjct: 63  KRYHYLLAQGTTGLSVAFDLPTQIGYDSDHEMADGEVGKVGVAIDSLKDIEILFDGIQLK 122

Query: 148 RISVSMTMNGAVIPILASFIVAGEEQGVSRDKLSGTIQNDILKEFMVRNTYIYPPEPSMR 207
            I+ SMT+N     +LA +I   ++QG    ++SGTIQNDILKE+  R TYIYPP+ SMR
Sbjct: 123 DITTSMTINATASILLAMYIALAKKQGADLKQISGTIQNDILKEYAARGTYIYPPKQSMR 182

Query: 208 IVADIIEYTAKEMPKFNSISISGYHMQEAGATLVQELAFTLADGREYVRAALAKGLNVDD 267
           ++ DI E+ +KE+PK+N+ISISGYH++EAG+T VQELAFTLA+G+ Y++AAL KGL+++ 
Sbjct: 183 LITDIFEFCSKEVPKWNTISISGYHIREAGSTAVQELAFTLANGKTYLKAALDKGLDINV 242

Query: 268 FAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIMQEFKPEKASSLMLRTHCQTSGVSLQEQ 327
           FA RLSFFF    NFF E AK RAAR +W +I ++       + MLR H QT G +L  Q
Sbjct: 243 FAKRLSFFFNCHNNFFEEIAKFRAARRMWAKITKDLGATDEKAQMLRFHTQTGGSTLTAQ 302

Query: 328 DPYNNIVRTAFEAMSAVLGGTQSLHTNSFDEAMALPTDFSARIARNTQLILQHETGVTKV 387
            P NN++R + +AM+AVLGGTQSLHTN +DEA++LPT+ +A+IA  TQ I+  E+GVT  
Sbjct: 303 QPLNNVIRVSNQAMAAVLGGTQSLHTNGYDEALSLPTESAAKIALRTQQIIAFESGVTDT 362

Query: 388 VDPLAGSYYVESLTNELAEKAWGLIEEVEALGGMTKAVNAGLPKRLIEEAATRRQAAVDR 447
           VDPLAGS++VE+LT+E+   AW  I+ ++A+GG   A+ +   +  I  A+ + Q  ++ 
Sbjct: 363 VDPLAGSFFVENLTDEVETAAWAYIDRIDAMGGSVNAIESDYMQNEIAGASYQYQKEIES 422

Query: 448 AEEVIVGVNKYRLENEQPIDILQIDNAAVRTAQVKRIEETRRRRDSQKMKQALDALADVA 507
            E + VGVNK+  E E   ++  ID+ ++R  Q +++E  +  RD+  +++AL +L + A
Sbjct: 423 GERISVGVNKFTQEEEGLTEVFNIDD-SIRKLQSEKLEILKTTRDNDAVEKALQSLHEAA 481

Query: 508 RSGKGNLLAAAVEAARARATVGEITDAMREAFGDY 542
           + G+ NL+   ++A    AT+GEI D  R  FG Y
Sbjct: 482 K-GETNLMPLIIDAVEKYATLGEIADVFRGTFGVY 515


Lambda     K      H
   0.318    0.134    0.379 

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: 810
Number of extensions: 29
Number of successful extensions: 2
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: 712
Length of database: 515
Length adjustment: 37
Effective length of query: 675
Effective length of database: 478
Effective search space:   322650
Effective search space used:   322650
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 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