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 GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein

Query= uniprot:A0A165KPY4
         (416 letters)



>FitnessBrowser__Phaeo:GFF3852
          Length = 409

 Score =  235 bits (600), Expect = 2e-66
 Identities = 141/411 (34%), Positives = 219/411 (53%), Gaps = 13/411 (3%)

Query: 3   KMTKIAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKG-HTWRDFAVAG 61
           K+T I        +A  A + ++EV H+WTSGGEA +V +    + G+  H W D A+AG
Sbjct: 2   KLTSILMTTALSVSATIAQSADLEVTHWWTSGGEAAAVTKFADAVNGQTTHNWVDGAIAG 61

Query: 62  GGGDSAMTVLKSRVISGNPPSAAQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELL-PKV 119
            G  +A  ++ SR++ G+P +A Q T G   +E    G++ ++  LA+ E W +++ P  
Sbjct: 62  SG-TTARPIIISRILGGDPMAATQLTHGRQAEELIEAGLMTDLTELAEQEGWRDIVNPPS 120

Query: 120 VADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVP 179
           + D   Y+G     PVN+H   W+W S EA  KAG++ +P+ W EF AAA KL  AG+VP
Sbjct: 121 LLDSCTYEGRIYCVPVNIHSTQWLWLSHEAFDKAGMS-VPQDWYEFVAAAPKLAEAGIVP 179

Query: 180 VAHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDP 239
           +A G Q WQ    F ++ +G+     ++   ++ D          K  +     +     
Sbjct: 180 LAMGQQGWQQRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDARELAR- 238

Query: 240 GAPGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVD 299
            +  +DWNLAT M+I GKAG Q+MGDWA+GEF  A +  G+D+ C    G       + D
Sbjct: 239 NSNVQDWNLATNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQIIDTSGD 298

Query: 300 SFILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKD 359
           +F    + DA  ++AQ D+AS ++S   Q  FNL KGS+PVR    +   +DC K     
Sbjct: 299 AFYFPVIDDAEVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGDVDLSAANDCMKKGLAI 358

Query: 360 FVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIA 410
             D    G ++PS     A +  T+  I+D++++FW  D ++ ADA  + A
Sbjct: 359 LAD----GNVLPSM--DQAFSADTQAQIQDLMAEFWASD-MAAADAQARYA 402


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: 469
Number of extensions: 22
Number of successful extensions: 7
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: 409
Length adjustment: 31
Effective length of query: 385
Effective length of database: 378
Effective search space:   145530
Effective search space used:   145530
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