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_058932055.1 AU252_RS18980 amino acid permease

Query= SwissProt::P46349
         (469 letters)



>NCBI__GCF_001484605.1:WP_058932055.1
          Length = 459

 Score =  344 bits (882), Expect = 4e-99
 Identities = 186/432 (43%), Positives = 270/432 (62%), Gaps = 6/432 (1%)

Query: 5   QSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLG 64
           +S L   +K R +TM+ +   IGAGLF+GSG+ I + GP  ++SY +AG L+I +M  LG
Sbjct: 11  ESHLGHTMKPRQLTMMGLGSAIGAGLFLGSGAGIQAAGPAVLISYLVAGTLIILVMWALG 70

Query: 65  EMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPL 124
           EM+A NPTSG+FS YA  A+G  AG T+GWL+W   V+VIA EA+  AG++   +  IP+
Sbjct: 71  EMAAANPTSGAFSVYAERALGKTAGATVGWLWWLQLVVVIAAEALGAAGLLFSVWPAIPV 130

Query: 125 WLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGF 184
           W  +L   +V T  N+  VK+FGEFE+WF+++KV  I+AFL VG A + G  P     G 
Sbjct: 131 WALALTFMVVFTAINLTGVKNFGEFEFWFAILKVAAIVAFLAVGAALLLGLLPDVASPGL 190

Query: 185 SNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRII 244
           +N+T    F P G+  V   + VVIF+F GTEIVA+AA ET +P  SV KA R+V+WRI+
Sbjct: 191 ANIT--TDFAPAGLGGVATALFVVIFAFGGTEIVAVAAAETEDPEHSVGKAIRTVLWRIL 248

Query: 245 VFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYT 304
           VFY+GS+ ++ A+LP +S   L SPF  VL+   +P A   +  + + A+LS LN+ LY 
Sbjct: 249 VFYIGSVFVIAAVLPVSSEG-LASPFAGVLDAARIPGAGTAITLVAVVALLSALNANLYG 307

Query: 305 TSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSS 364
            SRM+YSLAER EAPR   +LS   VP+ A+     F + A V+    PD +   L    
Sbjct: 308 ASRMVYSLAERGEAPRFLARLSGASVPMLAVGVSVAFGFFATVLELLFPDRILPALFQLV 367

Query: 365 GAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAF-ID 423
           G+  L+V+    VSQL +R++ ++   E L ++M  FP LT   ++ + G++ ++ F  +
Sbjct: 368 GSTCLVVWGTALVSQLILRRRADREGAE-LPLRMKGFPGLTICGLV-LLGLIFAIGFSAE 425

Query: 424 SMRDELLLTGVI 435
           S R +LL T V+
Sbjct: 426 SSRGQLLSTFVL 437


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: 582
Number of extensions: 29
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 469
Length of database: 459
Length adjustment: 33
Effective length of query: 436
Effective length of database: 426
Effective search space:   185736
Effective search space used:   185736
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