GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacH in Pseudomonas fluorescens FW300-N1B4

Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate Pf1N1B4_595 Glucose ABC transport system, inner membrane component 1

Query= uniprot:D4GP36
         (317 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_595
          Length = 314

 Score =  154 bits (388), Expect = 3e-42
 Identities = 91/272 (33%), Positives = 150/272 (55%), Gaps = 6/272 (2%)

Query: 44  VLMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVLLVG 103
           +++ +  YG   + F +SFT+   +  P Y  + L+ Y + + +D +  A++N  V    
Sbjct: 42  LIVLVGFYGYIIWTFVLSFTNSSFM--PSYKWVGLQQYIRLMDNDRWWVASKNLAVFGGM 99

Query: 104 FTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILNLVV 163
           F  I LVLG+FLA+LLD  IR     +TVYL PM+LS +VT   W W+ N   G L+ ++
Sbjct: 100 FIGISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWLLNPGLG-LDKML 158

Query: 164 TTLGFNP--VDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVDGAS 221
              G+    +DWL +    +  +++A +WQ SG+ M ++LAGL+ +      AA+VDGAS
Sbjct: 159 RDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQSIIRAAQVDGAS 218

Query: 222 ITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVRRAF 281
           +   YL+I++P L+    SA ++L   A+K+F  + A+     P   +D+ A  M    F
Sbjct: 219 LPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAG-GPGYSSDLPAMFMYSFTF 277

Query: 282 KFGEWAYSAAIATMLLIMALGVIGPYLYYQYK 313
             G+    +A A M+L   L ++ PYLY + +
Sbjct: 278 SRGQMGIGSASAMMMLGAILAILVPYLYSELR 309


Lambda     K      H
   0.326    0.140    0.424 

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: 294
Number of extensions: 19
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: 317
Length of database: 314
Length adjustment: 27
Effective length of query: 290
Effective length of database: 287
Effective search space:    83230
Effective search space used:    83230
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 (21.6 bits)
S2: 48 (23.1 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