GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_595 Glucose ABC transport
           system, inner membrane component 1
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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