GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Pseudomonas simiae WCS417

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF789 PS417_04010 glycine/betaine ABC transporter ATP-binding protein

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__WCS417:GFF789
          Length = 385

 Score =  198 bits (503), Expect = 3e-55
 Identities = 130/365 (35%), Positives = 207/365 (56%), Gaps = 24/365 (6%)

Query: 33  QILEKTGLSLG-----VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLI 87
           Q L KT  S G     V D SL + EGEI V +G SG GKST ++++NRLI+PT G++LI
Sbjct: 5   QNLSKTFQSNGKTVTAVNDVSLTVNEGEICVFLGPSGCGKSTTLKMINRLIKPTSGKILI 64

Query: 88  DGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALD 147
           +G D   + +  LR    + I  V Q   L P+MT+ +N     +L G + ++  ++A +
Sbjct: 65  NGEDTTDLDEVTLR----RNIGYVIQQIGLFPNMTIEENIVVVPKLLGWDKQKCHDRARE 120

Query: 148 ALRQVGLE--NYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQD 205
            +  + LE   Y H YP ELSGG +QR+G+ RALA +  +LLMDE F A+DP+ R  +Q+
Sbjct: 121 LMSMIKLEPKQYLHRYPRELSGGQQQRIGVIRALAADAPLLLMDEPFGAVDPINREMIQN 180

Query: 206 ELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF 265
           E  ++Q    +T++ +SHD+DEA+++GD+IAI + G+++Q+  PD +L +PA+++V  F 
Sbjct: 181 EFFEMQRALNKTVIMVSHDIDEAIKLGDKIAIFRAGKLLQIDHPDTLLAHPADEFVSNFV 240

Query: 266 RGVDIS----QVFSAKDIARRTPNGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFV 321
            G D +     +  A+D A   P+     +P      AL+L+ + DR Y  V    NK +
Sbjct: 241 -GQDSTLKRLLLVKAEDAADNAPS----VSPETPVADALELMDEHDRRYMVVTCAENKAL 295

Query: 322 GAVSIDSLKTALTQQQGLDAALIDAPLAVDAQTPLSELLSHVGQAPCA-VPVVDEDQQYV 380
           G V    L    T   G      +A  A D    L  LLS + +   + +PV+D ++ ++
Sbjct: 296 GYVRRRDLHRQ-TGTCGQYLREFNATAAYDEH--LRILLSRMYEFNRSWLPVMDAERVFL 352

Query: 381 GIISK 385
           G +++
Sbjct: 353 GEVTQ 357


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: 375
Number of extensions: 15
Number of successful extensions: 3
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: 385
Length adjustment: 31
Effective length of query: 369
Effective length of database: 354
Effective search space:   130626
Effective search space used:   130626
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 (21.7 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