GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Caulobacter crescentus NA1000

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  155 bits (392), Expect = 1e-42
 Identities = 84/239 (35%), Positives = 138/239 (57%), Gaps = 6/239 (2%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           I    + K +G+   + +++LTV+ GE   + GPSG GK+T++R +   E    G+I++D
Sbjct: 15  ITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILID 74

Query: 83  GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYL 142
           G     D+ N+   +  V MVFQ + +FPH+T+ +N+    + V  VPK E E      L
Sbjct: 75  G----QDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYG-LKVDNVPKAEREARVAEAL 129

Query: 143 EKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQ 202
           E V++     + P QLSGGQ+QRVA+AR+L  +P+++L DEP SALD ++ +++   +  
Sbjct: 130 ELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCT 189

Query: 203 LAEE-GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQI 260
           L E+ G+T + VTH+   A A+A+R   M+ G + +   P D +  P S     F+ Q+
Sbjct: 190 LQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQV 248


Lambda     K      H
   0.320    0.134    0.391 

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: 208
Number of extensions: 10
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: 263
Length of database: 381
Length adjustment: 27
Effective length of query: 236
Effective length of database: 354
Effective search space:    83544
Effective search space used:    83544
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: 48 (23.1 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