GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF295 PS417_01505 gamma-aminobutyrate
           transporter
          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.

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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