GapMind for catabolism of small carbon sources

 

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

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  150 bits (380), Expect = 3e-41
 Identities = 84/251 (33%), Positives = 146/251 (58%), Gaps = 13/251 (5%)

Query: 21  IAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKII 80
           +++ I Q+ + YG F  L D +L +  GE + + GPSGSGKS+++R +  L++   G ++
Sbjct: 1   MSLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVL 60

Query: 81  VDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLA---PIWVRKVPKREAEET 137
            DG    +DL  +   R ++G+VFQH+ LFPH+T+ +N+          R+  +R+    
Sbjct: 61  RDG----TDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAAR 116

Query: 138 AMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVL 197
               L +V++ E  ++YP QLSGGQ+QRVA+AR+L ++P ++L DEP  ALD + ++  L
Sbjct: 117 VEDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQ-VRGTL 175

Query: 198 DTMIQLAEE--GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQ 255
              ++  +   G+T + VTH+   A  +A+RV+ M  G+I +   P + +  P +     
Sbjct: 176 RVWLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHG 235

Query: 256 FL---SQILGH 263
           F+   ++I GH
Sbjct: 236 FVGRANRIRGH 246


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: 211
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: 384
Length adjustment: 27
Effective length of query: 236
Effective length of database: 357
Effective search space:    84252
Effective search space used:    84252
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