GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Pseudomonas stutzeri RCH2

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__psRCH2:GFF1860
          Length = 390

 Score =  173 bits (439), Expect = 7e-48
 Identities = 91/221 (41%), Positives = 139/221 (62%), Gaps = 6/221 (2%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           +KD +L I+ GE  +++G SG GKST++  +  L   T G++L+DG DI++ S  +    
Sbjct: 21  LKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGGEILVDGEDISQASPKD---- 76

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPD 163
             + IAMVFQS+AL P M+V DN AFG+++  + A +  E+     + + +E      P 
Sbjct: 77  --RDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVAKLLQIEPLLERKPS 134

Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223
           +LSGG +QRV + RALA  P I L DE  S LD  +R EM+ E+  +  + + T V+++H
Sbjct: 135 QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKLMHQRLKTTTVYVTH 194

Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
           D  EAM +GD++A+M++G + Q GTP EI NNPAN +V +F
Sbjct: 195 DQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASF 235


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: 378
Number of extensions: 17
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: 390
Length adjustment: 31
Effective length of query: 369
Effective length of database: 359
Effective search space:   132471
Effective search space used:   132471
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:

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