GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate Pf6N2E2_5395 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein

Query= uniprot:A0A1N7UK26
         (258 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5395
          Length = 244

 Score =  176 bits (446), Expect = 4e-49
 Identities = 91/234 (38%), Positives = 141/234 (60%), Gaps = 4/234 (1%)

Query: 25  KEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKCTWVHNEFDGMIPALRARK 84
           K +R G+   YPPF S  ++G + GFD ++GNA+CA+++VKC W+  EFDG+IPAL+ +K
Sbjct: 11  KTLRIGIEAAYPPFASKTSEGKIVGFDYDIGNALCAQMQVKCEWIEGEFDGLIPALKVKK 70

Query: 85  FDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPESLMGKQVGVLQGSLQE 144
            D  +SSM +T  R+K +DF+ + + + + ++ ++ A   D   +L GK VGV + +  +
Sbjct: 71  IDLALSSMTITEERKKSVDFTHKYYFTSSRLVMKEGAVVDDQYVNLKGKTVGVQRATTTD 130

Query: 145 AYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNFLSKPEGSDFK-TGP 203
            YA   L   G  +K Y + ++ Y DL +GRLDA   D +  + +FLS P G  +   GP
Sbjct: 131 RYATEVLEPKGVSVKRYSNNEEIYMDLASGRLDAIFADTIPLE-DFLSMPRGKGYAFVGP 189

Query: 204 AFKDPTLPLDIA-MGLRKNDQALRALINKGIAAVQADGTYAQIQKKYFGDQDIY 256
             KDP    + A + +RK +  L A +NK I  ++A+G Y +IQ KYF   DIY
Sbjct: 190 ELKDPKYVGEGAGIAVRKGNTQLVADLNKAIDGIRANGEYQKIQGKYF-KSDIY 242


Lambda     K      H
   0.319    0.135    0.393 

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: 161
Number of extensions: 8
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: 258
Length of database: 244
Length adjustment: 24
Effective length of query: 234
Effective length of database: 220
Effective search space:    51480
Effective search space used:    51480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

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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