GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5403 in Acidovorax sp. GW101-3H11

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate Ac3H11_1956 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1956
          Length = 252

 Score = 92.8 bits (229), Expect = 9e-24
 Identities = 50/133 (37%), Positives = 81/133 (60%), Gaps = 1/133 (0%)

Query: 240 IPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRV 299
           +P    + LAL  +T+A IAE VRSGI+++  GQ  A  ++G     T R V++P A R+
Sbjct: 108 VPGFALVVLALGFFTSARIAEQVRSGIQALPRGQRYAGMAVGFTTFQTYRYVLLPMAFRI 167

Query: 300 IIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISI 359
           IIPPLTS+ +N+ KNSS+A  +   E+ ++FA     +T + IEV     S+Y+  + +I
Sbjct: 168 IIPPLTSETMNIFKNSSVAFAVSVAEL-TMFAMQAQEETSRGIEVYLAVTSLYIISAFAI 226

Query: 360 SLLMNWYNKRIAL 372
           + +M +  KR+ +
Sbjct: 227 NRIMAFIEKRVRI 239



 Score = 50.4 bits (119), Expect = 5e-11
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 7/70 (10%)

Query: 73  TLLVTFIGVILATILGFIIGVARLSQNW-IISKLATVYVEVFRNIPPLLQILFWY----- 126
           T+ V+ + ++LA +LG +IG  R  Q+  +I +L   +VE+FRNIP L+QI  WY     
Sbjct: 41  TVSVSLLALVLALVLGSLIGTLRTLQDRPMIVRLGNAWVELFRNIPLLVQIFLWYHVIPS 100

Query: 127 -FAVFLSMPG 135
            F V   +PG
Sbjct: 101 LFPVMKGVPG 110


Lambda     K      H
   0.328    0.141    0.430 

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: 242
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 375
Length of database: 252
Length adjustment: 27
Effective length of query: 348
Effective length of database: 225
Effective search space:    78300
Effective search space used:    78300
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 (21.8 bits)
S2: 48 (23.1 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