GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Paucidesulfovibrio gracilis DSM 16080

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= CharProtDB::CH_001555
         (400 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  181 bits (459), Expect = 3e-50
 Identities = 89/239 (37%), Positives = 149/239 (62%), Gaps = 6/239 (2%)

Query: 26  EQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQV 85
           E  +  + ++++ G ++ V++  L IE GE+  ++G SG GK+T++R++  L  PT+G +
Sbjct: 42  EPAVRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDI 101

Query: 86  LIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKA 145
            I G    +I+D     + ++ + M+FQ++AL PH T+ +N AFG++   ++ EE REK 
Sbjct: 102 YIKG---RRINDTP---IHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKV 155

Query: 146 LDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQD 205
             AL  V L      Y  +LSGG +QR+ LARA+ I PD+LLMDE  SALD  +R EM+ 
Sbjct: 156 AQALEMVRLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRM 215

Query: 206 ELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
           E+  +Q +   T +F++HD  EA+ + ++I +M++G   Q GTP+++ + P N +V  F
Sbjct: 216 EIDNIQQQLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADF 274


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: 358
Number of extensions: 11
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: 406
Length adjustment: 31
Effective length of query: 369
Effective length of database: 375
Effective search space:   138375
Effective search space used:   138375
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 Apr 09 2024. 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