GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01112 in Caulobacter crescentus NA1000

Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= reanno::Burk376:H281DRAFT_01112
         (364 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  133 bits (334), Expect = 8e-36
 Identities = 101/305 (33%), Positives = 150/305 (49%), Gaps = 16/305 (5%)

Query: 54  TVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAA 113
           T+  +++   + GA N RF       ++L   +   + A+G   V+  GGIDV+  ++ A
Sbjct: 28  TILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLA 87

Query: 114 LTMYGITKAVFAWWPDAP--FALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYL 171
                    V A   D P  + + L+   L G+  G V G  V  L  P+ IVT+G   +
Sbjct: 88  FASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTV 147

Query: 172 YRG--LLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWW 229
           +RG  LLL   G     N  +     G I          L   +PV + ALVAAA     
Sbjct: 148 WRGATLLLNDGGPISGFNDAYRWWGSGEI----------LFLPVPVVIFALVAAAGHV-- 195

Query: 230 LLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPF 289
            L  T  GR VYA+GG+   A   G N+  I   V+   G LAG++G L  +    A   
Sbjct: 196 ALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAV 255

Query: 290 DLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGA 349
              G EL VIA+V++GGA +TGG+G V GT+LG +L+ ++ + L+++ V S  Q+V+IG 
Sbjct: 256 AGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGL 315

Query: 350 FILLA 354
            I+ A
Sbjct: 316 IIVAA 320


Lambda     K      H
   0.328    0.141    0.426 

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: 301
Number of extensions: 16
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: 364
Length of database: 332
Length adjustment: 29
Effective length of query: 335
Effective length of database: 303
Effective search space:   101505
Effective search space used:   101505
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: 49 (23.5 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