GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Salinicoccus carnicancri Crm

Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein

Query= SwissProt::Q8U259
         (348 letters)



>NCBI__GCF_000330705.1:WP_017549841.1
          Length = 338

 Score =  168 bits (426), Expect = 2e-46
 Identities = 118/335 (35%), Positives = 176/335 (52%), Gaps = 15/335 (4%)

Query: 5   MVAIMKTKPEYGAELVEVDVPKPGPG-EVLIKILATSICGTDLHIYEWNEWAQTRIRPPQ 63
           M AI   KP     +VE++ P    G EV++KI    ICG+D+HIY  +    +    P+
Sbjct: 1   MKAIQVEKPGQ-LNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNPFTSY---PR 56

Query: 64  IMGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDG 123
           ++GHEV+G V +VG  V  +  GD V++E    CG+CYAC+ GQ +VC + ++FGV  DG
Sbjct: 57  VIGHEVSGIVEQVGEAVTSLAPGDLVALEPITYCGECYACRNGQPNVCDSLEVFGVHRDG 116

Query: 124 VFAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPI-AGKSVLITGAGPLGLL 182
             AEY      N  K P N+  E A L EP+         G +  G +V + GAGP G+ 
Sbjct: 117 GMAEYLKADENNWHKVPGNVSEEAAALMEPMTIGAQATYRGDVREGDTVFVIGAGPTGIA 176

Query: 183 GIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLE 242
            +  AK  GA  V +S+ ++ R + AK +GAD  I P    V +E+  +T+G   +V ++
Sbjct: 177 CLLQAKQRGA-KVFISDFNQNRLDYAKSIGADATIQPDGVHVEEEINRLTNGELANVVID 235

Query: 243 FSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYT 302
             G P+  +Q ++  + AGRV  LG      SI  + L+  K L V G       +T   
Sbjct: 236 AVGLPQTFQQAVELASIAGRVVTLGFNEQPSSIP-SLLLTKKELKVAG----SRLQTHQF 290

Query: 303 VSRLLQSGKLNIDP--IITHKYKGFDKYEEAFELM 335
              + Q G+  IDP  II+ +Y   D+  +AFEL+
Sbjct: 291 PKVIDQVGRGEIDPTQIISQRY-SMDQIHDAFELL 324


Lambda     K      H
   0.318    0.138    0.417 

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: 276
Number of extensions: 15
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: 348
Length of database: 338
Length adjustment: 29
Effective length of query: 319
Effective length of database: 309
Effective search space:    98571
Effective search space used:    98571
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: 49 (23.5 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