GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Marinobacter adhaerens HP15

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__Marino:GFF3087
          Length = 256

 Score =  256 bits (653), Expect = 4e-73
 Identities = 135/250 (54%), Positives = 181/250 (72%), Gaps = 9/250 (3%)

Query: 6   APLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRL 65
           +PLI  D + K F  L+VL+G++ E    DV+S+IG SG GKSTFLRC+N LE  + G +
Sbjct: 5   SPLICRD-IYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSGDI 63

Query: 66  EVAG------VDLSGAKI--DQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLR 117
            V G       +  G +I  D K +  +R ++ MVFQ FNL+ H+TVL+N++ AP  VL+
Sbjct: 64  IVHGDPIRFTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHVLK 123

Query: 118 IPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSAL 177
           +P  EA +RA  YL+KVG+  + D YP Q+SGGQ+QR AIAR L M+PE++LFDEPTSAL
Sbjct: 124 VPKKEAIERAEAYLNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTSAL 183

Query: 178 DPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNP 237
           DPELVGEVL VM+ LAEEG TM VVTHEM FAR+VS++V F +QG+IEE+G P +VF +P
Sbjct: 184 DPELVGEVLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFDHP 243

Query: 238 KSDRLRAFLS 247
            S+R++ FL+
Sbjct: 244 DSERMKQFLT 253


Lambda     K      H
   0.321    0.139    0.397 

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: 216
Number of extensions: 6
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: 252
Length of database: 256
Length adjustment: 24
Effective length of query: 228
Effective length of database: 232
Effective search space:    52896
Effective search space used:    52896
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 (21.9 bits)
S2: 47 (22.7 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