GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsA in Marinobacter adhaerens HP15

Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF3014 HP15_2958 extracellular solute-binding protein family 1

Query= uniprot:A0A165KPY4
         (416 letters)



>lcl|FitnessBrowser__Marino:GFF3014 HP15_2958 extracellular
           solute-binding protein family 1
          Length = 416

 Score =  452 bits (1162), Expect = e-131
 Identities = 224/410 (54%), Positives = 284/410 (69%), Gaps = 6/410 (1%)

Query: 3   KMTKIAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGG 62
           K    AAV+  L  A +  AGEVEVLH+WT+GGEA++   LK++M+ +GHTW+DFAVAGG
Sbjct: 8   KTLTAAAVSAALLPAQALQAGEVEVLHWWTAGGEARAAVALKEMMEDQGHTWKDFAVAGG 67

Query: 63  GGDSAMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVAD 122
           GG++AMTVLK+R +SGNPP+AAQ KG  I+EWA  G L ++D +A+A  W +L+P V+AD
Sbjct: 68  GGEAAMTVLKTRAVSGNPPAAAQIKGLDIREWAKLGFLTSLDDVAEANNWGQLIPPVIAD 127

Query: 123 VMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAH 182
           VM+Y+ +YVA PVNVHRVNW+W + E L K GV  +PKT DEF+ AA+KLKAAG+ P+AH
Sbjct: 128 VMQYEDSYVAVPVNVHRVNWLWANPETLNKVGVG-VPKTLDEFYQAAEKLKAAGITPLAH 186

Query: 183 GGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAP 242
           GGQ WQD T FE+V L V G   +  A V+ D   + S  M++    F ++  Y D  A 
Sbjct: 187 GGQPWQDATVFEAVALAVMGPDDFASAFVEHDMDVINSAQMEEVFAEFAKVMSYVDDNAA 246

Query: 243 GRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFI 302
           GRDWN AT M+I+G+A  Q+MGDWAKGEF AAG  PG+D++CAAAPG+   FTFNVDSF 
Sbjct: 247 GRDWNTATGMVIRGEAAMQIMGDWAKGEFTAAGLTPGEDYVCAAAPGTGGQFTFNVDSFA 306

Query: 303 LFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVD 362
           +F L D    KAQ DLA +IM P FQ VFN  KGSIPVR       FD CA+AS   F  
Sbjct: 307 MFSLSDEDNTKAQKDLARTIMEPEFQAVFNKAKGSIPVRT-----DFDTCAQASMDTFKS 361

Query: 363 TAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAA 412
           +A+ GGLVPS AHG+A     +G I DVV+ F N D    A A  ++AAA
Sbjct: 362 SAEDGGLVPSFAHGLATTSYVQGQIFDVVTNFVNSDNKDPARATDQLAAA 411


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: 599
Number of extensions: 26
Number of successful extensions: 3
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: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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