GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Dechlorosoma suillum PS

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::Q9RW56
         (523 letters)



>FitnessBrowser__PS:Dsui_0105
          Length = 476

 Score =  214 bits (546), Expect = 4e-60
 Identities = 157/473 (33%), Positives = 225/473 (47%), Gaps = 23/473 (4%)

Query: 38  KHYPLIIDGQEVDTEGK--IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKW 95
           +H    I GQ V  +G   I   NP  T  V+    + T  DA+ A + A  AF +W   
Sbjct: 3   QHSRFYIGGQWVAPDGNAFIDVENPA-TETVIARVPEGTATDADRAARAAAAAFPAWAAL 61

Query: 96  DMDARARILLKAAAILKRRRLEACALMSIEVGKNYAEAD-VEVAEAIDFLEYYARSAMKY 154
               R   L K A  LK R+ E   L++ EVG     A  V+    I      AR A + 
Sbjct: 62  SGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE- 120

Query: 155 AGFGSSETTWFEGEENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAED 214
            GF           ++ ++ +P G    I+PWNFP         A + AG  VV+KP+E 
Sbjct: 121 -GFAEERIG-----QSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEV 174

Query: 215 AGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEV 274
           A L A  + +++  AGLPAGV   + G G  VGE L  H     ++FTGS A G  +  V
Sbjct: 175 APLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAV 234

Query: 275 AAKVQPGQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVV 334
           AA        +KRV +ELGGK   +V   AD+  A+     G F  +GQ CSA++RL+V 
Sbjct: 235 AAAT------VKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVP 288

Query: 335 DSVYDEVVNGFVERAKALKMGTG-EENANVTAVVNQMSFNKIKGYLELAPSEGKVLLGGE 393
              Y E     V+ A A  +G    E + +  +V+ +   +++  +E A ++G  LL G 
Sbjct: 289 QERYAEAAALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGG 348

Query: 394 ATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLT 453
           +        GYY++PT+ G V  ++ LA+EE+FGPV+A+L  +D  +A  IAN T+YGL 
Sbjct: 349 SAAPEGLPTGYYVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLA 408

Query: 454 GGVCSNSRERLEQARAEFEVGNLYFNRKITGAIVG-VQPFGGYNMSGTDSKAG 505
             V S    R          G +     I GA    + PFGG+  SG   + G
Sbjct: 409 AAVWSAEEARALAFARRLRAGQV----DINGAFFNLLAPFGGFKQSGYGRELG 457


Lambda     K      H
   0.317    0.134    0.391 

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: 561
Number of extensions: 25
Number of successful extensions: 4
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: 523
Length of database: 476
Length adjustment: 34
Effective length of query: 489
Effective length of database: 442
Effective search space:   216138
Effective search space used:   216138
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 (21.6 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