GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Dyella japonica UNC79MFTsu3.2

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  218 bits (556), Expect = 2e-61
 Identities = 128/301 (42%), Positives = 176/301 (58%), Gaps = 21/301 (6%)

Query: 19  SLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQI 78
           SL ++ + + +G+   L    LD+ +GEFV  +GPSG GKS+LLR +AGL+D   G V  
Sbjct: 2   SLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLR 61

Query: 79  DGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLK---QAGVP-KAEIEEKVAKAA 134
           DG ++  +   +R I +VFQ YAL+PH+TV DN+  GL+   +A  P + +I  +V    
Sbjct: 62  DGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLL 121

Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194
             + LE    R P +LSGGQRQRVA+ RA+  EP L L DEP   LDA +R   R+ +  
Sbjct: 122 RRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRD 181

Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQ 254
           L RSL  T + VTHDQ EA+ LAD++VV+N GRIEQVG+P E+Y  PA  FV GF+G   
Sbjct: 182 LQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRAN 241

Query: 255 --MNFIEAAKL------------GD--GEAKTIGIRPEHIGL-SRESGDWKGKVIHVEHL 297
                +E  +L            GD  G      +RPEH+ L SR  G W G++ H++  
Sbjct: 242 RIRGHVERDRLHLGGHSFQGELPGDLAGREIEAWLRPEHLALASRGLGGWTGRLQHLDLA 301

Query: 298 G 298
           G
Sbjct: 302 G 302


Lambda     K      H
   0.320    0.137    0.393 

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: 356
Number of extensions: 16
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: 352
Length of database: 384
Length adjustment: 30
Effective length of query: 322
Effective length of database: 354
Effective search space:   113988
Effective search space used:   113988
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: 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