GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Sinorhizobium meliloti 1021

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate SMc00094 SMc00094 betaine aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Smeli:SMc00094
          Length = 487

 Score =  265 bits (676), Expect = 3e-75
 Identities = 165/476 (34%), Positives = 252/476 (52%), Gaps = 9/476 (1%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65
           K  ++I+GE+VE       + + PAT E++ ++  +T   ++ A   A  A   W+ ++ 
Sbjct: 6   KASHFIDGEYVEDAAGTVIESIYPATGEIIARLHAATPGIVEKAIAAAKRAQPEWAAMSP 65

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAG-APSLMM 123
             R RIL    +L+ Q   EL+ L T++ GK  +E +  +   G ++ EF  G AP+ + 
Sbjct: 66  TARGRILKRAAELMRQRNRELSELETLDTGKPIQETIVADPTSGADSFEFFGGVAPAALN 125

Query: 124 GDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPL 183
           GD +  +  D  A   R P+GV  GI  +N+P  + CW    A+  GN  + KPSE TPL
Sbjct: 126 GDYIP-LGGDF-AYTKRVPLGVCVGIGAWNYPQQIACWKGAPALVAGNAMVFKPSENTPL 183

Query: 184 LTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSEN 243
              K+ E+  +AGLPKG+FNV+ G       ++ HP++  +S  GS P G+ V    +  
Sbjct: 184 GALKIAEILIEAGLPKGLFNVIQGDRATGPLLVNHPDVAKVSLTGSVPTGKKVAGAAAAE 243

Query: 244 LKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAK 303
           LK V    G K+  IV +DA+LE  +   +   F S G+ C     V V+  I + F+A+
Sbjct: 244 LKHVTMELGGKSPLIVFDDADLESAIGGAMLGNFYSTGQVCSNGTRVFVQRKIKEPFLAR 303

Query: 304 LQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG--RENVSDDG 361
           L+E+   I IG+ LD+   LGP++    + +  SYI KG  EGARLV  G    NVS +G
Sbjct: 304 LKERTEAIVIGDPLDEATQLGPMVSAAQRDKVFSYIGKGKAEGARLVTGGGIPNNVSGEG 363

Query: 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421
            ++ PT+F +VT  MTI ++EIF PV+ V+   +  E I  AN +EF   A +FT++   
Sbjct: 364 TYIQPTVFADVTDGMTIAREEIFGPVMCVLDFDDEVEVIARANATEFGLSAGVFTADLTR 423

Query: 422 IRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477
                + ++AG L IN     P+   PF G K S FG    N   +++ YT  K V
Sbjct: 424 AHRVADRLEAGTLWINTYNLCPVE-IPFGGSKQSGFG--RENSVAALNHYTELKTV 476


Lambda     K      H
   0.318    0.136    0.396 

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: 558
Number of extensions: 36
Number of successful extensions: 3
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: 487
Length of database: 487
Length adjustment: 34
Effective length of query: 453
Effective length of database: 453
Effective search space:   205209
Effective search space used:   205209
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: 52 (24.6 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