GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Dinoroseobacter shibae DFL-12

Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3607519 Dshi_0931 Alcohol dehydrogenase GroES domain protein (RefSeq)

Query= reanno::Cup4G11:RR42_RS34260
         (342 letters)



>FitnessBrowser__Dino:3607519
          Length = 339

 Score =  426 bits (1095), Expect = e-124
 Identities = 221/337 (65%), Positives = 250/337 (74%), Gaps = 2/337 (0%)

Query: 3   AMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLPFI 62
           +MMKAA+V +F  PL I EV  P    G I VKIEA GVCHTDLHAA GDWPVKP  PFI
Sbjct: 2   SMMKAALVTDFSKPLEIREVRKPTVTDGNILVKIEACGVCHTDLHAARGDWPVKPEPPFI 61

Query: 63  PGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQ-QNTGYSVN 121
           PGHEGVG V  VG  V+ VKEGDRVGVPWL+ ACG+C  C+ GWETLC  + + TGY+VN
Sbjct: 62  PGHEGVGVVVEVGHNVTSVKEGDRVGVPWLHHACGHCTACVTGWETLCRTEPEYTGYTVN 121

Query: 122 GGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGLG 181
           GG+ EYV ADP YVG LPD + F   APILCAGVTVYKGLK  D  PGQ VVISGIGGLG
Sbjct: 122 GGFAEYVEADPTYVGHLPDKLDFAPAAPILCAGVTVYKGLKECDLHPGQTVVISGIGGLG 181

Query: 182 HVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFLQKEIGGAHGALVT 241
           H+AVQYARAMGL V AVD+ + KL LAR LGA V +NA T DPVA + + +GGA G LVT
Sbjct: 182 HLAVQYARAMGLHVIAVDVAEDKLALARDLGAGVAINAATQDPVAEVAR-LGGAEGVLVT 240

Query: 242 AVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQESLD 301
           AVS  AF Q +GM+  GGT++L GLPPGDFP  IFDVVL   TIRGSIVGTR+DL ESL 
Sbjct: 241 AVSNTAFSQGVGMLAPGGTMSLVGLPPGDFPLNIFDVVLNRKTIRGSIVGTRADLAESLS 300

Query: 302 FAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVM 338
           FAA G V +  +T  L+ IN IF +M  G IEGR+VM
Sbjct: 301 FAAEGKVASHYATDSLDNINGIFDQMEQGRIEGRIVM 337


Lambda     K      H
   0.319    0.138    0.420 

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: 412
Number of extensions: 16
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: 342
Length of database: 339
Length adjustment: 28
Effective length of query: 314
Effective length of database: 311
Effective search space:    97654
Effective search space used:    97654
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 (21.7 bits)
S2: 49 (23.5 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