GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Thiothrix lacustris DSM 21227

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  152 bits (383), Expect = 1e-41
 Identities = 84/222 (37%), Positives = 127/222 (57%), Gaps = 6/222 (2%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           +  VSL+I +G+  V +G SG GKSTL+R I  L     G+++ DG +I ++        
Sbjct: 19  IKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILDGRDITEVPPS----- 73

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPH 162
             R ++MVFQS+AL PH TV +N+ +  R+  V     +E      D + L+ Y  + P 
Sbjct: 74  -QRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADKLNLTAYLQRTPK 132

Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITH 222
            LSGG +QRV + R++     V L DE  S LD  +RG+ + ++  L R L  T V++TH
Sbjct: 133 ALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLHRELGATTVYVTH 192

Query: 223 DLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
           D  EA+ +   + +LRDG + QVGTP ++ D P N +VARF+
Sbjct: 193 DQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFI 234


Lambda     K      H
   0.323    0.139    0.397 

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: 254
Number of extensions: 13
Number of successful extensions: 2
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: 275
Length of database: 348
Length adjustment: 27
Effective length of query: 248
Effective length of database: 321
Effective search space:    79608
Effective search space used:    79608
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 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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