GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Dinoroseobacter shibae DFL-12

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 3608030 Dshi_1437 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Dino:3608030
          Length = 351

 Score =  293 bits (749), Expect = 5e-84
 Identities = 152/262 (58%), Positives = 195/262 (74%), Gaps = 1/262 (0%)

Query: 4   IEIRNVYKIFGHDAKKALTMVED-GLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLS 62
           IEI NV+KIFG +A+ AL  V D GL KA+IL+     VG+ DVSL +  G+IF IMGLS
Sbjct: 7   IEISNVWKIFGANAQAALEAVRDRGLSKAEILAEFNAVVGVADVSLSVRRGEIFCIMGLS 66

Query: 63  GSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTV 122
           GSGKSTLVRH NRL+EPT+G +  +G +++ LG + L+ FR R++ MVFQ+FALMPHR+V
Sbjct: 67  GSGKSTLVRHFNRLLEPTAGRIEIEGTDVMALGTQELQRFRNRQIGMVFQNFALMPHRSV 126

Query: 123 LQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADT 182
           L NV     +R V K++        +D V L  + AKF H+L GGM+QRVGLARALAA+ 
Sbjct: 127 LDNVAMPLEIRKVPKNERMRQAAAILDIVELGAWGAKFAHELPGGMQQRVGLARALAANP 186

Query: 183 DVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQV 242
           DV+LMDE FSALDPLIR  +QD+ ++L + L KT +FITHDLDEA+RIG  IAI+RDG+V
Sbjct: 187 DVLLMDEPFSALDPLIRRQLQDEFIRLSKILKKTTIFITHDLDEAVRIGDRIAIMRDGKV 246

Query: 243 VQVGTPNDILDNPANDYVARFV 264
           VQ+GT  DI+ +PA+DYVA FV
Sbjct: 247 VQMGTAEDIVMHPADDYVADFV 268


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: 326
Number of extensions: 6
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: 351
Length adjustment: 27
Effective length of query: 248
Effective length of database: 324
Effective search space:    80352
Effective search space used:    80352
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 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