GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS25460
          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:

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