GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter (characterized, see rationale)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25895
          Length = 367

 Score =  372 bits (954), Expect = e-107
 Identities = 197/362 (54%), Positives = 258/362 (71%), Gaps = 4/362 (1%)

Query: 1   MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60
           M  LK+ N+ K   G  I++ + LE+   EFVVFVGPSGCGKSTLLRLIAGL+ +  G +
Sbjct: 1   MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTI 60

Query: 61  LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120
            +DGR + ++ P +R + MVFQ+YALYPHMSV  N+SF L LA  +K  + ++V + A+I
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARI 120

Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180
           L+L  +L+RKPK+LSGGQRQRVA+GRA+ R P I LFDEPLSNLDA+LRVQMR E+ARLH
Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180

Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240
             L +TMIYVTHDQVEAMTLADK+VVLNGGR+EQVGSP ELY +PA+ FVAGFLG+P+M 
Sbjct: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240

Query: 241 FLSARLQTPGETSLVDTLVWGIT--SLPFDSSNLAAGTPLSLGIRPEHVSLK-AADGTAG 297
           FL  ++ T  E    + L+   T  +LP   +NL+ G  ++LGIRPEH++L    D T  
Sbjct: 241 FLKGKV-TRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCTLQ 299

Query: 298 VVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVAL 357
           V     E LGS+T+ H+ T   E L  R       + G+++ L LD ++ HLFDA+GVA+
Sbjct: 300 VTADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDANGVAV 359

Query: 358 SR 359
           +R
Sbjct: 360 AR 361


Lambda     K      H
   0.320    0.137    0.394 

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: 378
Number of extensions: 13
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: 381
Length of database: 367
Length adjustment: 30
Effective length of query: 351
Effective length of database: 337
Effective search space:   118287
Effective search space used:   118287
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: 50 (23.9 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