GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Ochrobactrum thiophenivorans DSM 7216

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate WP_094509348.1 CEV31_RS18520 amino acid ABC transporter permease

Query= uniprot:Q31RN9
         (396 letters)



>NCBI__GCF_002252445.1:WP_094509348.1
          Length = 214

 Score =  118 bits (295), Expect = 2e-31
 Identities = 68/203 (33%), Positives = 119/203 (58%), Gaps = 6/203 (2%)

Query: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVM 249
           G   TL  +L++ V    LG+L+A+ R S    IR+ S  Y+++ +G PL+  L      
Sbjct: 13  GATWTLGLSLVAFVGGGLLGLLIAVSRVSKSRIIRYSSFLYVQIIQGTPLLIQLLLAYFG 72

Query: 250 VPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYR 309
           + L+    + I     A + + ++ SAY  E  RGG+ ++P+ Q+EAA  L L+ FQ + 
Sbjct: 73  LSLI---GFDIPPFAAASLAIAVYASAYFGEIWRGGILSVPKTQWEAAECLALSSFQRFW 129

Query: 310 FIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLF 369
            +++PQALR+S P  VG  + ++++T+L S++G+ +L   S+ ++ N  +  +  +V++ 
Sbjct: 130 LVIVPQALRLSTPPTVGFMVQIVKNTSLASVIGVADLTYTSK-LINNSTF--QPFQVFVL 186

Query: 370 LGVLYWLCCYGLAQLSRRLEQRL 392
           +  LY+L CY LA  SR+LE RL
Sbjct: 187 VAALYFLMCYPLAWWSRKLEDRL 209


Lambda     K      H
   0.329    0.142    0.471 

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: 211
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: 396
Length of database: 214
Length adjustment: 26
Effective length of query: 370
Effective length of database: 188
Effective search space:    69560
Effective search space used:    69560
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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