GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Phaeobacter inhibens BS107

Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF1918 PGA1_c19500 putative sugar-binding periplasmic protein

Query= uniprot:A0A165KPY4
         (416 letters)



>FitnessBrowser__Phaeo:GFF1918
          Length = 414

 Score =  271 bits (693), Expect = 3e-77
 Identities = 149/416 (35%), Positives = 231/416 (55%), Gaps = 14/416 (3%)

Query: 2   WKMTKIAAVA-VGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVA 60
           +K   +A VA + + +A +A     EV+H+W S GEA ++          G  W D  + 
Sbjct: 3   FKSNLLAGVATLAMTSAATADGIRAEVIHWWVSAGEAAAIKVFADAYTANGGEWIDNGIG 62

Query: 61  GGGGDSAMTVLKSRVISGNPPSAAQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELLPKV 119
           GGG   A T   +R++ G+ P   Q       +E    G+L ++D  A+A  W  L P +
Sbjct: 63  GGG---AKTTFVNRLMGGDAPQVGQFNTSREFEEIVDAGLLHSLDAEAEAGNWSALFPGI 119

Query: 120 VADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVP 179
           + +V+K  G+Y A PVN+H  NW+W +++ +  AG+  +P  WD FF AA+ LK AG++P
Sbjct: 120 IDNVVKRDGSYYAVPVNIHGSNWLWHNNQVMADAGLD-VPTDWDSFFEAAETLKEAGIIP 178

Query: 180 VAHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGY--- 236
           +A GG+ WQ+  TF SV+L VGG   Y     + D TALTSD MK+  + + R++     
Sbjct: 179 LAVGGEAWQERLTFNSVLLSVGGQDLYLRLFEEKDTTALTSDEMKEVFDVYSRLRTLVRE 238

Query: 237 TDPGAPGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTF 296
           TDPG+PGR WN AT M+I G+A  Q+MGDWAKGEFL+AG  PG ++ C  A  + + +  
Sbjct: 239 TDPGSPGRSWNDATNMVITGQAAMQIMGDWAKGEFLSAGMTPGVEYGCTPAVIAGSPYMI 298

Query: 297 NVDSFILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKAS 356
           + D F+  K  +   ++AQS +A++++    Q  FN  KGSIPVR      + D C + +
Sbjct: 299 SGDVFVFPKTGNEEDREAQSLMATTMLDAEVQVAFNNIKGSIPVRPDVDTSQLDVCGQQA 358

Query: 357 AKDFVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAA 412
                +     G+       M I+    GA++DV +QFWN + ++  +A+  ++ A
Sbjct: 359 IALTSNPDTHVGVTQ-----MYISSDLAGALQDVYTQFWNSETMTTEEAITLLSQA 409


Lambda     K      H
   0.315    0.128    0.383 

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: 503
Number of extensions: 17
Number of successful extensions: 5
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: 416
Length of database: 414
Length adjustment: 31
Effective length of query: 385
Effective length of database: 383
Effective search space:   147455
Effective search space used:   147455
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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