GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Caulobacter crescentus NA1000

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Caulo:CCNA_00647
          Length = 261

 Score =  134 bits (338), Expect = 2e-36
 Identities = 72/191 (37%), Positives = 117/191 (61%), Gaps = 6/191 (3%)

Query: 25  NLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMVFQ 84
           +L I   EF   +G SGCGK+T L ++AGL  +T G + +  + VN   P   D A+VFQ
Sbjct: 29  DLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTTGAVILDRQEVNAPGP---DRAVVFQ 85

Query: 85  NYALYPHMTVYQNMAFGL-KLRKVPKAEIDRR--VQEAAKILDIAHLLDRKPKALSGGQR 141
           N++L P ++V +N++  + K+    K+  +R+  V    +++ + H LD++P  +SGG +
Sbjct: 86  NHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWVLHNLELVKMTHALDKRPAEISGGMK 145

Query: 142 QRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMT 201
           QRV + RA+  EP+V L+DEP   LDA  R  ++  + ++H  L+ TV+ +THD  EA  
Sbjct: 146 QRVGIARALSMEPKVLLLDEPFGALDALTRAHLQDSVMEIHSALKNTVLMITHDVDEATL 205

Query: 202 MGDRIVVMRDG 212
           + DRIV+M +G
Sbjct: 206 LSDRIVMMTNG 216


Lambda     K      H
   0.321    0.138    0.395 

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: 211
Number of extensions: 6
Number of successful extensions: 3
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: 384
Length of database: 261
Length adjustment: 27
Effective length of query: 357
Effective length of database: 234
Effective search space:    83538
Effective search space used:    83538
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