GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Caulobacter crescentus NA1000

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  218 bits (554), Expect = 3e-61
 Identities = 115/237 (48%), Positives = 160/237 (67%), Gaps = 3/237 (1%)

Query: 9   VEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVN 68
           V K +G +  + N++L + +GE    +GPSGCGK+TLLRM+AG E  T G + IDG  ++
Sbjct: 20  VTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILIDGQDIS 79

Query: 69  DVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLD 128
           +VPP +R + MVFQSYA++PHMTV +N+++ LK+    +AE +A V  A E +QLG    
Sbjct: 80  NVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQLGGLGG 139

Query: 129 RLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTM 188
           R P  LSGGQRQRVA+ R++V+ P+V L DEPLS LDA LR   R E+  L+E +   T 
Sbjct: 140 RKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKV-GITF 198

Query: 189 VYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPG 245
           + VTHDQ EA+ LA+R  V++ G + QV +P +LYE P + FVA FIG  ++NL  G
Sbjct: 199 IMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIG--QVNLFEG 253


Lambda     K      H
   0.316    0.135    0.379 

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: 359
Number of extensions: 18
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: 373
Length of database: 381
Length adjustment: 30
Effective length of query: 343
Effective length of database: 351
Effective search space:   120393
Effective search space used:   120393
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: 41 (21.6 bits)
S2: 50 (23.9 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