GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Pseudomonas stutzeri RCH2

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF17 Psest_0017 ectoine/hydroxyectoine ABC transporter, permease protein EhuD

Query= uniprot:Q31RN9
         (396 letters)



>FitnessBrowser__psRCH2:GFF17
          Length = 219

 Score =  111 bits (277), Expect = 2e-29
 Identities = 64/201 (31%), Positives = 110/201 (54%), Gaps = 6/201 (2%)

Query: 192 LLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVP 251
           L T+  AL     ++ LG+ LA+GR+S L  + W     IE  R  PL+  ++F   + P
Sbjct: 21  LTTIGIALAGFAIAVVLGLFLAIGRRSRLRWLSWPITGLIEFIRSTPLLIQVYFLFYVFP 80

Query: 252 LMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFI 311
              +    +  +   I+G+ +  + Y AE  R GL A+P+ Q+EA  AL +  +  YR +
Sbjct: 81  ---NYGLNLSAMQAGIIGIALHYACYTAEVYRAGLDAVPRSQWEAVTALNMKPWTAYRDV 137

Query: 312 VLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLFLG 371
           +LPQALR  +PA+    +++L+DT +LS + ++E++  +++I +      RY E    +G
Sbjct: 138 ILPQALRPVLPALGNYLISILKDTPVLSAITVVEIMQRAKNIGSESF---RYLEPITMVG 194

Query: 372 VLYWLCCYGLAQLSRRLEQRL 392
           + + +   GLA   RRLE R+
Sbjct: 195 IFFLILSLGLAWCVRRLENRM 215


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: 231
Number of extensions: 10
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: 219
Length adjustment: 26
Effective length of query: 370
Effective length of database: 193
Effective search space:    71410
Effective search space used:    71410
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 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