GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Epibacterium ulvae U95

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_090218033.1 CV091_RS10640 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_002796795.1:WP_090218033.1
          Length = 483

 Score =  246 bits (629), Expect = 1e-69
 Identities = 143/469 (30%), Positives = 235/469 (50%), Gaps = 4/469 (0%)

Query: 9   NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68
           N I G W     D+ E+       +++     ++ + +D     A  A   W+   + R+
Sbjct: 7   NLIAGSWTVG-VDEIENRNPSDLSDLVGMFAQASSDQLDATLDQAKIAQAEWAAYGIERK 65

Query: 69  ARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLA 128
             +L      +    EEL  L++ E GK   E  GEV R  +   + A      +G++  
Sbjct: 66  YNVLMAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAETLRQIGENAD 125

Query: 129 SIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKL 188
           S+   +E    R  +G V  I+P+NFP     W    A+  GN  + KP+  TP     L
Sbjct: 126 SVREGIEIDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANATPASAVAL 185

Query: 189 VELFEKAGLPKGVFNVVYGA-HDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRV 247
            E+ E+  +PKG+F++V GA  ++   ++E  ++ AISF GS PVG+ +     +NL +V
Sbjct: 186 TEIIERQDIPKGLFSLVMGAGREIGQRLVESSKVDAISFTGSVPVGKGIASAAIQNLTKV 245

Query: 248 QSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEK 307
           Q   G+KN   V++DA+++  V+  +G AFG  G++C A + + V   + DEF++KL   
Sbjct: 246 QMEMGSKNALAVMDDADIDLAVSLALGGAFGGTGQKCTASSRLVVHSAVHDEFVSKLVAG 305

Query: 308 VADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFVGP 366
              +K+G+ L+ G  +GPV+ E      L+Y++ G  EGA L+C G R  +   GY++ P
Sbjct: 306 AKAMKVGHALEAGTQIGPVVTEQQLNENLAYVDLGKSEGAELLCGGQRLEMPHQGYYMNP 365

Query: 367 TIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFR 426
            IF   T +M I ++E+FAP+ +VI+V    EA+ + N + F   + + T +     +FR
Sbjct: 366 GIFIGTTNDMRINREEMFAPLAAVIKVSGYDEALSVVNDTNFGLTSGIVTKSLARANHFR 425

Query: 427 ENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
            N   G + +NL         PF G   S +G     GK + +FYT  K
Sbjct: 426 RNAQTGCVMVNLPTAGTDYHVPFGGRGDSSYGP-REQGKAAAEFYTTVK 473


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: 527
Number of extensions: 21
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: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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 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