GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF3014
          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:

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