GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dmeA in Phaeobacter inhibens BS107

Align Possible transporter of polar amino acids including glutamate, glutamine and aspartate, DmeA. It complements a sepJ mutation in Anabaena (TC# 2.A.7.23.2), and SepJ complements a dmeA mutation. Alternatively, and less likely, it could be an activator of an ABC transporter catalyzing uptake of these amino acids (characterized)
to candidate GFF3374 PGA1_c34270 putative integral membrane protein

Query= TCDB::Q31PG5
         (330 letters)



>FitnessBrowser__Phaeo:GFF3374
          Length = 294

 Score = 80.9 bits (198), Expect = 4e-20
 Identities = 81/283 (28%), Positives = 130/283 (45%), Gaps = 15/283 (5%)

Query: 21  SLQLAIATA-LWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLLLIL-WQREGWPPLNRR 78
           +L + +A A +W   FT+ RI V   SPL     R+L++  + + +  +  + W  L R 
Sbjct: 5   ALAMGLAFAFMWSSAFTSARIIVADASPLYSLAFRFLISGLIGVAVARYMGQSWR-LTRG 63

Query: 79  QQLLLFGLGVSGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQW 138
           Q       G+   ALY  L F+ +  I AS AA+I +  P  +A+   +  G+RL     
Sbjct: 64  QLKATVIFGICQNALYLGLNFVAMETIEASLAAIIASTMPMLVAIALWLVYGERLPRLGV 123

Query: 139 AGVGLSLIGAILLLGSRQAGALTLPGWGDLALVGC-VLCWTVYSLLARQALRSLSPLTVT 197
            G+   ++G  L++G+R +  + L G   + L G  VL  T+ +L  R A    + + V 
Sbjct: 124 VGLLAGVLGVALIMGTRISAGVDLFG---VLLCGIGVLALTLATLALRGATSGGNYMMVV 180

Query: 198 TGACCWGSVLLIGLWLGQGAQLPVNVSFSTGSAIAFLGLGGTALAFCLYANGIERLGAAR 257
                 GS +L  +         +  S+    A  +  L     A  ++   + R+GA R
Sbjct: 181 GLQMLIGSAVLF-VVAPMVETFRLTPSWPLALAFVYTTLVPGLTATFIWVLLLNRIGAVR 239

Query: 258 AGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGVGLGT 300
           A  F  L PVFG A+ ++LL E L       GLL + GVG+ T
Sbjct: 240 AATFHFLNPVFGVAVASVLLGEQL-------GLLDIVGVGIVT 275



 Score = 28.5 bits (62), Expect = 2e-04
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 92  ALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWAGVGLSLIGAILL 151
           A + W+    L+ I A RAA    LNP      A++  G++L      GVG+   G + +
Sbjct: 224 ATFIWVLL--LNRIGAVRAATFHFLNPVFGVAVASVLLGEQLGLLDIVGVGIVTFGILAV 281

Query: 152 LGSRQAGALT 161
             +RQ+   T
Sbjct: 282 QLARQSAQRT 291


Lambda     K      H
   0.325    0.142    0.454 

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: 262
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 330
Length of database: 294
Length adjustment: 27
Effective length of query: 303
Effective length of database: 267
Effective search space:    80901
Effective search space used:    80901
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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