GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Herbaspirillum seropedicae SmR1

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate HSERO_RS07530 HSERO_RS07530 amino acid ABC transporter permease

Query= TCDB::A1VZQ3
         (250 letters)



>FitnessBrowser__HerbieS:HSERO_RS07530
          Length = 216

 Score =  130 bits (328), Expect = 2e-35
 Identities = 74/208 (35%), Positives = 111/208 (53%), Gaps = 4/208 (1%)

Query: 37  ALDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPL 96
           + DN    +    +TL +S LA L   I G I  +M TS    +R  + +Y+++ Q  P+
Sbjct: 6   SFDNFVFLLEAARWTLLLSALAFLGGGIAGFIVALMRTSHLAPLRLLSAVYIQIIQGTPV 65

Query: 97  VIQIFFLFYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGF 156
           +I +F  FY L + G +L       + +  Y  AY+ E+ R  I AVP  Q+EAS +   
Sbjct: 66  LILLFLSFYGLAIFGYKLPPMVAATIAMTIYSSAYLGEIWRGCIEAVPVPQWEASTALAM 125

Query: 157 TYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAP 216
           T  QQ+RY+I+PQ +RI LPP    +V ++KNTS+  I+G  EL  +          + P
Sbjct: 126 TRWQQLRYVILPQAVRISLPPTVGFLVQIVKNTSIASIIGLVELAQAGK--LVSNATFQP 183

Query: 217 AYIFAAV--LYFIICYPLAYFAKAYENK 242
             +F  V  +YF+ CYPL+ FA A E K
Sbjct: 184 FLVFPIVAGIYFVFCYPLSRFAFALERK 211


Lambda     K      H
   0.328    0.143    0.422 

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: 138
Number of extensions: 5
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: 250
Length of database: 216
Length adjustment: 23
Effective length of query: 227
Effective length of database: 193
Effective search space:    43811
Effective search space used:    43811
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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