GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Pseudomonas fluorescens GW456-L13

Align ABC transporter permease (characterized, see rationale)
to candidate PfGW456L13_4608 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4608
          Length = 307

 Score =  252 bits (643), Expect = 9e-72
 Identities = 140/302 (46%), Positives = 197/302 (65%), Gaps = 15/302 (4%)

Query: 6   QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAP 65
           QQ++NGL +GS YALIA+GYTMVYGII +INFAHGEV MIG+  ++  I  +  AM G  
Sbjct: 9   QQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL--AMLGLD 66

Query: 66  GWVILLLATIIAC-VVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124
              +L+ A  +A  VV +   + IE++AYRPLR S RL PLI+AIGMSI LQ   ++   
Sbjct: 67  SVPLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLAQD 126

Query: 125 PNYKPYPTMLPSS-PFEIGGA---FITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180
              K  P ++P +  F  GGA    I+  QI++  VT VA+  L   ++ + LGRA RA 
Sbjct: 127 SKDKSIPNLIPGNFAFGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRAC 186

Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240
           AE+ ++A+L+G+  + +I+ TF+IGA LAAIA ++ +  YG      GFL GLKAFTAAV
Sbjct: 187 AEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAV 246

Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
            GGIG++ GA++GG++LG+ EA G+         + G  Y D+ AF +L+++L  RP+GL
Sbjct: 247 LGGIGSIPGAMLGGLVLGVAEAFGA--------DIFGDQYKDVVAFGLLVLVLLFRPTGL 298

Query: 301 LG 302
           LG
Sbjct: 299 LG 300


Lambda     K      H
   0.327    0.142    0.419 

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: 266
Number of extensions: 13
Number of successful extensions: 4
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: 309
Length of database: 307
Length adjustment: 27
Effective length of query: 282
Effective length of database: 280
Effective search space:    78960
Effective search space used:    78960
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 (21.7 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