GapMind for catabolism of small carbon sources

 

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

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate H281DRAFT_00987 H281DRAFT_00987 glycine betaine/proline transport system ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00987 H281DRAFT_00987 glycine
           betaine/proline transport system ATP-binding protein
          Length = 429

 Score =  370 bits (951), Expect = e-107
 Identities = 204/391 (52%), Positives = 268/391 (68%), Gaps = 3/391 (0%)

Query: 5   LEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64
           L VKNL KIFG  P+RA + I +GL + +I E+TG  + V D SL+++ GEIFV+MGLSG
Sbjct: 38  LTVKNLSKIFGPRPERAAELIRQGLGRNEIFEQTGNMVAVNDVSLSVKAGEIFVVMGLSG 97

Query: 65  SGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVL 124
           SGKST+VRLLNRLIEPT GQV+++G DIA +S  ELR+VRRKK+AMVFQSFAL+P+ TVL
Sbjct: 98  SGKSTLVRLLNRLIEPTSGQVILEGRDIAPMSTPELRDVRRKKMAMVFQSFALLPNRTVL 157

Query: 125 DNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPD 184
           DN A+G+E+AG+   ER + A  AL +VGL +Y    P ELSGGM+QRVGLARALA+NP 
Sbjct: 158 DNIAYGLEVAGLKKAERYDIARAALTRVGLGSYEKLLPGELSGGMQQRVGLARALAVNPS 217

Query: 185 ILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVV 244
           +LLMDEAFSALDPLIR EMQ EL++LQ + QRTIVFISHD++EA++IG RI IM++G ++
Sbjct: 218 VLLMDEAFSALDPLIRFEMQSELLRLQKEEQRTIVFISHDIEEAIKIGGRIGIMKDGCLI 277

Query: 245 QVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLLQ 304
           QVGTP E++ +PA+DYVR FFR VD+S+   A  +  R    LI           L  L 
Sbjct: 278 QVGTPAELIQSPADDYVRDFFRNVDVSRFLKASSLMTRVERELISCDVAAPSERYLNQLI 337

Query: 305 DEDREYGYVIERGNKFVGVVSIDSLKAALSQAQGIEAALIDDPLVVDAQTPLSELLSHVG 364
           D   + GYV +   ++ G V+  SL+   + A  I  A ++D   V     L +L +   
Sbjct: 338 DSGADCGYVCDEAGRYQGCVTPASLRK--TGAHSIREAFVNDVNAVPLDADLHQLATIAL 395

Query: 365 QAPCAVPVVDEEHQYVGIISKRMLL-QALDR 394
                VPV D   +  GI+S R +L Q ++R
Sbjct: 396 NQQHDVPVTDTAGRLAGIVSCRAILKQVMER 426


Lambda     K      H
   0.319    0.137    0.378 

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: 465
Number of extensions: 14
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: 400
Length of database: 429
Length adjustment: 31
Effective length of query: 369
Effective length of database: 398
Effective search space:   146862
Effective search space used:   146862
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 (21.8 bits)
S2: 50 (23.9 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