GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proY in Pseudomonas simiae WCS417

Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate GFF295 PS417_01505 gamma-aminobutyrate transporter

Query= SwissProt::P46349
         (469 letters)



>FitnessBrowser__WCS417:GFF295
          Length = 463

 Score =  469 bits (1208), Expect = e-137
 Identities = 239/456 (52%), Positives = 323/456 (70%), Gaps = 2/456 (0%)

Query: 3   QSQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRM 62
           QS + L++ LK RH+TM+SIAGVIGAGLFVGSG  I + GP  +++YA AG LV+ +MRM
Sbjct: 5   QSSNDLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGTLVVLVMRM 64

Query: 63  LGEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDI 122
           L EM+  +P +GSFS YA  AIG WAGFTIGWLYW+FWV+VI +EA A A I+  WF DI
Sbjct: 65  LAEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPDI 124

Query: 123 PLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPV 182
            +W+ +L++T++LT TN++SVK++GEFE+WF+LIKVV I+ F+I+G A IFGF P S+  
Sbjct: 125 AIWVFTLVITLLLTATNLFSVKNYGEFEFWFALIKVVAIVGFVILGLAAIFGFLPTSQVS 184

Query: 183 GFSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWR 242
           G S+L    GF P G+ +VL  I+  +FSFMGTEIV IAA E+ NP + +TKAT SV+WR
Sbjct: 185 GVSHLFDTQGFMPNGMGAVLAAILTTMFSFMGTEIVTIAAAESKNPGQQITKATNSVIWR 244

Query: 243 IIVFYVGSIAIVVALLPWNSANILE-SPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSG 301
           I +FY+ SI IVV+L+PWN   +     +  VLE +G+P A  I++ +VL AV SCLNS 
Sbjct: 245 IGLFYLLSIFIVVSLVPWNDPTLAAVGSYQTVLERMGIPNAKLIVDLVVLVAVTSCLNSA 304

Query: 302 LYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLV 361
           LYT SRML+SL  R +AP    + +K G P  A++  T  +++AV  NY +P  VF FL+
Sbjct: 305 LYTASRMLFSLGRRGDAPAVAKRTNKSGTPYWAVLLSTGAAFLAVFANYVAPAAVFEFLL 364

Query: 362 NSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAF 421
            SSGAIALLVYLVIAVSQL+MR+K      E +  KMWLFP LTY  ++ I G L  M F
Sbjct: 365 ASSGAIALLVYLVIAVSQLRMRQKRTAAG-EKIVFKMWLFPGLTYAVMVFIVGTLTIMLF 423

Query: 422 IDSMRDELLLTGVITGIVLISYLVFRKRKVSEKAAA 457
            ++ R E++ TGV++ +V+ + L    R+ +++A A
Sbjct: 424 QEAHRIEIIATGVLSLLVVAAGLFVSSRRKTQRAGA 459


Lambda     K      H
   0.326    0.140    0.417 

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: 631
Number of extensions: 21
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: 469
Length of database: 463
Length adjustment: 33
Effective length of query: 436
Effective length of database: 430
Effective search space:   187480
Effective search space used:   187480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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