GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Caulobacter crescentus NA1000

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  227 bits (578), Expect = 5e-64
 Identities = 126/294 (42%), Positives = 180/294 (61%), Gaps = 5/294 (1%)

Query: 4   LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFID 63
           +  +++ K +G +  +  + L + EGEF   +GPSGCGK+TLLRM+AG E  T G + ID
Sbjct: 15  ITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILID 74

Query: 64  GERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQL 123
           G+ +++VPP+KR + MVFQSYA++PHMTV DN+A+G+++    K E + RV  A +++QL
Sbjct: 75  GQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQL 134

Query: 124 TPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERM 183
                R P  LSGGQRQRVA+ RA+ + P+V L DEPLS LDA LR   R E+  L E++
Sbjct: 135 GGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKV 194

Query: 184 SDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVI 243
              T I VTHDQ EA+ LA R  V+S G ++QV  P +LYE P + FVA FIG   +N+ 
Sbjct: 195 G-ITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQ--VNLF 251

Query: 244 PATITATGQQTAVSLAGGKSVTLDVPTNAS-ENGKTASFGVRPEDLRV-TEADD 295
              +       AV  +    V + +    +   G T    +RPE + +  +ADD
Sbjct: 252 EGVLAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWAAIRPEKIELHKKADD 305


Lambda     K      H
   0.320    0.137    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: 345
Number of extensions: 15
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: 362
Length of database: 381
Length adjustment: 30
Effective length of query: 332
Effective length of database: 351
Effective search space:   116532
Effective search space used:   116532
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 (21.8 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