GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Pseudomonas stutzeri RCH2

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>FitnessBrowser__psRCH2:GFF4241
          Length = 335

 Score =  183 bits (464), Expect = 5e-51
 Identities = 101/226 (44%), Positives = 141/226 (62%), Gaps = 2/226 (0%)

Query: 45  VVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDAL 104
           V  +    L I +GE+F ++G SG+GKSTL+R  NRL +P+ G ILV+GED+  LD D L
Sbjct: 18  VPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGRILVNGEDVTALDADGL 77

Query: 105 REFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRG-ESKQVCAERALHWINTVGLKGYEN 163
           R FR+ ++ M+FQ F LL  K+V DNVA  L++ G  S++    R    +  VGLK +  
Sbjct: 78  RRFRQ-RVGMIFQHFNLLMSKTVADNVAMPLRLAGIRSRREIDARVAALLERVGLKEHAR 136

Query: 164 KYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIV 223
           KYP QLSGG +QRVG+ARALA +  I+L DEA SALDP   A +   L E+ + L  TIV
Sbjct: 137 KYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIV 196

Query: 224 FITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269
            ITH++D   R+ +R+A++  G +++ G   E+   P      RFV
Sbjct: 197 LITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFLHPKHPTTQRFV 242


Lambda     K      H
   0.321    0.138    0.387 

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: 232
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: 276
Length of database: 335
Length adjustment: 27
Effective length of query: 249
Effective length of database: 308
Effective search space:    76692
Effective search space used:    76692
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 (21.9 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