GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases

Query= reanno::acidovorax_3H11:Ac3H11_612
         (483 letters)



>FitnessBrowser__Cola:Echvi_3822
          Length = 453

 Score =  229 bits (584), Expect = 1e-64
 Identities = 144/461 (31%), Positives = 237/461 (51%), Gaps = 17/461 (3%)

Query: 27  STNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQRRADVLDMIGSELLARKD 86
           S NP  T E++ E+      Q E A++   +A  +W +    +RAD++   G  L    D
Sbjct: 3   SINPY-TGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNTD 61

Query: 87  ELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELLASVRQGVQVDVTREPVG 146
           + G +++ E GK + E  +EV +   + +++A  A  +  +   ++  G +  V   P+G
Sbjct: 62  KYGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPLG 121

Query: 147 VVGIIAPWNFPFAIPAWKI----APALAYGNTVVFKPAELVPACGWALAEIISRSGLPAG 202
           +V  + PWNFPF    W++    AP L  GN  + K A  VP C  A+ E+ +++G P G
Sbjct: 122 IVLAVMPWNFPF----WQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEG 177

Query: 203 AF-NLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAKVQLEMGGKNPLI 261
            F +L++GS +     ++ HP V A + TGS   G +I   A ++  K  LE+GG +P I
Sbjct: 178 VFQSLLIGSDKVAN--IIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFI 235

Query: 262 VLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRNRLASLKVGHALE 321
           VL DAD+ +A   A +G   + GQ C A+ R I+E EV+D F+   ++ + S   G  L+
Sbjct: 236 VLKDADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLD 295

Query: 322 RGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGHYMSP-ALFLARPEHR 380
                  +   +   +    ++ +  +GAE +  G + E+     ++ P  L    P+  
Sbjct: 296 EKAGYACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKA--FIKPYILGKLTPDMP 353

Query: 381 VAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFKRHAAVGMTMVN 440
             REE+FGPVA V +A+D D A+A+AND+ FGL A + T   ++A    R    G   +N
Sbjct: 354 AYREELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFIN 413

Query: 441 LPTAGVDFHVPFGGRKESSYGAREQGRYAAEFYTTVKTGYM 481
              A  + ++PFGG K+S YG RE      + +  +KT Y+
Sbjct: 414 SMVAS-NPYLPFGGIKKSGYG-RELAENGIKEFMNIKTVYL 452


Lambda     K      H
   0.320    0.135    0.400 

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: 429
Number of extensions: 13
Number of successful extensions: 5
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: 483
Length of database: 453
Length adjustment: 33
Effective length of query: 450
Effective length of database: 420
Effective search space:   189000
Effective search space used:   189000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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