GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsB in Sinorhizobium meliloti 1021

Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate SM_b21377 SM_b21377 sugar uptake ABC transporter substrate-binding protein precursor

Query= CharProtDB::CH_003593
         (296 letters)



>FitnessBrowser__Smeli:SM_b21377
          Length = 296

 Score =  162 bits (409), Expect = 1e-44
 Identities = 104/292 (35%), Positives = 158/292 (54%), Gaps = 8/292 (2%)

Query: 1   MNMKK-LATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNL 59
           MNM + L TLV+  AL  T+ A+    D I   + T  +PF++ L +  + EA +    L
Sbjct: 1   MNMPRILKTLVAGTAL--TLLASGAFADGIGASLLTQQHPFYIELAEAMKAEAKEKNVAL 58

Query: 60  VVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATK 119
            V  +  +  K+LA+V+D  V+G  +++I+P DS  V  A+  A +A I VIT+D  A  
Sbjct: 59  EVAIANQDLNKQLADVEDFIVKGVDVIVISPVDSQGVRAAIAKAEKAGIKVITVDVPANG 118

Query: 120 GEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKF 179
             V SHI +DN  GG  AG+ +A+  G   KV  +       +   R  GF++A+A H  
Sbjct: 119 ATVTSHIGTDNFTGGVKAGELMAEVLGNKGKVAIID-YPTVQSVVNRVNGFKEAIAKHPE 177

Query: 180 NVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAG-KSDVMVVG 238
             + +      R + L   QN+L A+PD+  +F   D+ AL A  A++ AG +S V V+G
Sbjct: 178 MEIVATQTGITRAEALAAAQNMLQANPDITGIFGFGDDAALAAAVAVKAAGLESQVKVIG 237

Query: 239 FDGTPDGEKAVNDGK--LAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPV 288
           FDG  +   AV DG   +   I Q PDQ+G + ++TA KV+ GE V A+ P+
Sbjct: 238 FDGMKEARDAV-DGNPVMVGVIQQFPDQMGKQAIDTAVKVVAGETVPAEQPI 288


Lambda     K      H
   0.313    0.129    0.344 

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: 225
Number of extensions: 14
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: 296
Length of database: 296
Length adjustment: 26
Effective length of query: 270
Effective length of database: 270
Effective search space:    72900
Effective search space used:    72900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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