GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutV in Paraburkholderia bryophila 376MFSha3.1

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate H281DRAFT_02450 H281DRAFT_02450 glycine betaine/proline transport system ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02450 H281DRAFT_02450 glycine
           betaine/proline transport system ATP-binding protein
          Length = 393

 Score =  275 bits (703), Expect = 1e-78
 Identities = 137/262 (52%), Positives = 193/262 (73%)

Query: 4   IEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSG 63
           + +  + K+FG + K+AL M+  G  K ++ +R+G  VG+++VS ++  G+IFV+MGLSG
Sbjct: 6   VVVEGLCKVFGTNPKQALAMLAGGATKEEVFARTGQIVGVHNVSFEVKEGEIFVLMGLSG 65

Query: 64  SGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVL 123
           SGKSTL+R INRL+EP++G+VL DG ++  +    L A R + +SMVFQSFALMP RTVL
Sbjct: 66  SGKSTLIRLINRLVEPSAGKVLIDGRDVASVPRAELTALRRKDMSMVFQSFALMPQRTVL 125

Query: 124 QNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTD 183
            N  +G  V GVS+ +     M  ++ VGL+ + AK P QLSGGM+QRVGLARALA +  
Sbjct: 126 SNAAFGLEVAGVSRKEREARAMTVLEQVGLAPFAAKLPAQLSGGMQQRVGLARALAVNPS 185

Query: 184 VILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVV 243
           +++MDEAFSALDPL R +MQ+ LL LQR   +TI+F++HDL+EA+RIG+ IAI+  G+VV
Sbjct: 186 LMIMDEAFSALDPLKRKEMQNVLLDLQREQQRTILFVSHDLEEAMRIGTRIAIMEGGKVV 245

Query: 244 QVGTPNDILDNPANDYVARFVQ 265
           Q+GTP +I+ NPA+DYV  F +
Sbjct: 246 QIGTPQEIITNPADDYVRAFFE 267


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: 313
Number of extensions: 8
Number of successful extensions: 1
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: 393
Length adjustment: 28
Effective length of query: 247
Effective length of database: 365
Effective search space:    90155
Effective search space used:    90155
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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