GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potD in Phaeobacter inhibens BS107

Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF3389 PGA1_c34420 putrescine-binding periplasmic protein PotF

Query= SwissProt::Q02UB7
         (367 letters)



>FitnessBrowser__Phaeo:GFF3389
          Length = 361

 Score =  380 bits (976), Expect = e-110
 Identities = 194/359 (54%), Positives = 249/359 (69%)

Query: 8   TLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLE 67
           TL  +TL   VA  + AA  + + VYNWSDYI  D LEKF  ETGI ++YDV+DSNE+LE
Sbjct: 2   TLKTMTLTAIVALSSAAAVAEEVRVYNWSDYIDEDLLEKFETETGIDLIYDVFDSNELLE 61

Query: 68  AKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEH 127
            K+LAG SGYDVVVP+ SFLA+QI+AG +QKLD SKL N  N+   +       DP N +
Sbjct: 62  TKMLAGGSGYDVVVPTGSFLARQIQAGAFQKLDTSKLSNAGNMWDVIEDRTARYDPDNLY 121

Query: 128 AIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPA 187
           ++ YMWGT GIG N  KV+ A G +AP+DS +LVF P+NI+KL  CGV FLD+P E++PA
Sbjct: 122 SVNYMWGTTGIGANTAKVEEALGADAPIDSLELVFNPDNIEKLANCGVYFLDAPDEMIPA 181

Query: 188 ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQ 247
           AL Y+G  P++ +P  +  AE + + IRPYV  FHSS+YI+ LANG+ICVA G+SGDI Q
Sbjct: 182 ALKYIGEDPNSMDPDVVAKAEPVLMAIRPYVKKFHSSEYINALANGDICVAFGWSGDILQ 241

Query: 248 AKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITD 307
           A+ RA+EA N V + +N PKEGA  +FD +AIP DA N +GA  F+NF+M+ E MA  ++
Sbjct: 242 ARDRADEADNGVEIVFNAPKEGALMWFDQMAIPVDAPNPDGAHKFLNFIMEAENMAAASN 301

Query: 308 VVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSG 366
            V + NGN A+   + E +  DP IYPSEE +K LY     P K QR  TR WTKIKSG
Sbjct: 302 YVYYANGNKASQEFLEEDVIGDPAIYPSEETLKNLYIKEAYPPKVQRKATRMWTKIKSG 360


Lambda     K      H
   0.315    0.133    0.390 

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: 452
Number of extensions: 17
Number of successful extensions: 2
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: 367
Length of database: 361
Length adjustment: 29
Effective length of query: 338
Effective length of database: 332
Effective search space:   112216
Effective search space used:   112216
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: 42 (22.0 bits)
S2: 49 (23.5 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