GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Caulobacter crescentus NA1000

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  191 bits (485), Expect = 3e-53
 Identities = 115/298 (38%), Positives = 171/298 (57%), Gaps = 28/298 (9%)

Query: 3   TLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNL 62
           T+ + ++ K++   ++ ++   +L+I D E +  +GPSG GK+T LR IAGLE    G +
Sbjct: 2   TIAIRSVEKQF--GRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQV 59

Query: 63  YIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYK----KDDINKRVHE 118
             D + +  AS   R +  VFQ YAL+ HM+V +N+AFGL +RK K    K +I +RV E
Sbjct: 60  LFDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEE 119

Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178
             +++ L     R P+ LSGGQRQRVA+ RA+     V L+DEP   LDA +R ++R E+
Sbjct: 120 LLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRREL 179

Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPA 238
            ++H   G TTI+VTHDQ EA+ LADR+ I++           GRIEQIGTP ++++ P 
Sbjct: 180 RRVHDATGVTTIFVTHDQEEALELADRVAILNN----------GRIEQIGTPDQVHDAPE 229

Query: 239 NKFVAGFIGSPAMNFFEVTVEKERL----------VNQDGLSLALPQGQEKILEEKGY 286
             FV GF+G    N F+  V   R             +DG + A  +  +  L+E G+
Sbjct: 230 TAFVCGFVGE--ANRFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGF 285


Lambda     K      H
   0.318    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: 292
Number of extensions: 10
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: 377
Length of database: 339
Length adjustment: 29
Effective length of query: 348
Effective length of database: 310
Effective search space:   107880
Effective search space used:   107880
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 (21.7 bits)
S2: 49 (23.5 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