GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proY in Pseudarthrobacter sulfonivorans Ar51

Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease

Query= SwissProt::P46349
         (469 letters)



>NCBI__GCF_001484605.1:WP_058929813.1
          Length = 470

 Score =  369 bits (947), Expect = e-106
 Identities = 195/455 (42%), Positives = 285/455 (62%), Gaps = 4/455 (0%)

Query: 4   SQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRML 63
           S   L   LK R +TM+ +   IGAGLF+GSG+ I + GP  ++SY +AG L+I +M  L
Sbjct: 8   SGRALGAALKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPAVLISYLVAGTLIILVMWAL 67

Query: 64  GEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIP 123
           GEM+A NP SG+FS Y   A GP AG T+GWL+W   V+VIA EA+  AG++   F  +P
Sbjct: 68  GEMAAANPDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPALP 127

Query: 124 LWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVG 183
           +WL + +  +VLT  N+ SVK+FGEFE+WF+L+KV  I+ FL+VG A +FG+ PG +  G
Sbjct: 128 VWLMAFVFIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQSPG 187

Query: 184 FSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRI 243
            +N TG  GF P+G + +   + VV F+F GTEIV++AA ET+ P  SV  A R+V+WRI
Sbjct: 188 LANFTG-DGFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLWRI 246

Query: 244 IVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLY 303
           +VFY+G+I ++ A++P  SA  L+SPF AVLE  G+P AA  +  + + A+LS LN+ LY
Sbjct: 247 LVFYIGAIFVIAAVVPVGSAG-LKSPFAAVLEAAGMPGAATAITLVAVAALLSALNANLY 305

Query: 304 TTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNS 363
             SRM YSLA+R EAPR    +SK  VPV A++A   F  + VV+    P+ V   L+N 
Sbjct: 306 GASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFPEKVLPVLLNI 365

Query: 364 SGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFID 423
            G+  LLV+    ++QL +R +  +   E L ++M  FP+LT   ++ +  I       +
Sbjct: 366 VGSTCLLVWTSALLAQLALRLRANREGTE-LPLRMPGFPWLTCFGLLILAAIFTVGFIGE 424

Query: 424 SMRDELLLTGVITGIVLI-SYLVFRKRKVSEKAAA 457
             R +LL T  +  ++ + ++L  R  KV+ +  A
Sbjct: 425 DSRPQLLSTFALVALLAVANWLHHRSGKVAGRVEA 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: 621
Number of extensions: 30
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: 470
Length adjustment: 33
Effective length of query: 436
Effective length of database: 437
Effective search space:   190532
Effective search space used:   190532
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 Apr 09 2024. 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