GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Caulobacter crescentus NA1000

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  238 bits (607), Expect = 2e-67
 Identities = 125/252 (49%), Positives = 174/252 (69%), Gaps = 8/252 (3%)

Query: 4   LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63
           +T ++VTK +     G + AV+ +SL +++GEF  L+GPSGCGK+T LRM+AG ET TEG
Sbjct: 15  ITFENVTKRF-----GKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEG 69

Query: 64  ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123
            + ++ + ++ V    R + MVFQSYA++PH +V  N+++GL+    +P  E   RV E 
Sbjct: 70  RILIDGQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDN-VPKAEREARVAEA 128

Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183
            +++ +  L  RKP QLSGGQ+QRVAL RA+V+ P V L+DEPLS LDAKLR +MRTEL 
Sbjct: 129 LELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELC 188

Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243
            LQ ++G+T + VTHDQ EA+ +  R AV+  G LQQV TP D Y  PN+ FVA FIG+ 
Sbjct: 189 TLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQ- 247

Query: 244 SMNLFDGSLSGD 255
            +NLF+G L+ D
Sbjct: 248 -VNLFEGVLAVD 258


Lambda     K      H
   0.316    0.136    0.384 

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: 376
Number of extensions: 19
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: 383
Length of database: 381
Length adjustment: 30
Effective length of query: 353
Effective length of database: 351
Effective search space:   123903
Effective search space used:   123903
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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