GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Phaeobacter inhibens BS107

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF2520 PGA1_c25590 putative glycine betaine/L-proline transport system, ATP binding subunit

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__Phaeo:GFF2520
          Length = 350

 Score =  275 bits (703), Expect = 1e-78
 Identities = 139/278 (50%), Positives = 198/278 (71%), Gaps = 1/278 (0%)

Query: 4   KLEIKNLYKIFGEHPQRAFKYIE-QGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGL 62
           K++I+NLYKIFG +P      +  QG+ K Q+LE+    LG++D S+ I+ GEI VIMGL
Sbjct: 5   KIQIRNLYKIFGANPGTVLPMVRNQGMGKSQLLEEHKHVLGLQDISIDIQAGEISVIMGL 64

Query: 63  SGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMT 122
           SGSGKST++R LNRLIEPT G++L+DG D+  +   +LRE+R++ ++MVFQ FAL+PH T
Sbjct: 65  SGSGKSTLIRHLNRLIEPTAGEILLDGQDVMDLDPVQLREMRQRSMSMVFQKFALLPHKT 124

Query: 123 VLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAIN 182
           VL+N    + + G +       A   L +VGL  + + YP +LSGGM+QRVG+ARAL  +
Sbjct: 125 VLENAETALRVRGDDRATCEAAARKWLDRVGLSGFENRYPSQLSGGMQQRVGIARALTAD 184

Query: 183 PDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGE 242
            DI+L+DEAFSALDPLIRT+MQD L++LQ +  +TIVFI+HDLDEA+++ D + I+++G 
Sbjct: 185 TDIMLLDEAFSALDPLIRTDMQDLLLELQTELHKTIVFITHDLDEALKLADHLVILKDGA 244

Query: 243 VVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIA 280
           VVQ G P  I+ NPA+ Y+  F   ++ ++V  A  IA
Sbjct: 245 VVQQGPPQGIVMNPADPYIEAFVGDINRARVLRAGTIA 282


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: 381
Number of extensions: 15
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: 350
Length adjustment: 30
Effective length of query: 370
Effective length of database: 320
Effective search space:   118400
Effective search space used:   118400
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