GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AGP1 in Pseudomonas stutzeri RCH2

Align general amino acid permease AGP1 (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases

Query= CharProtDB::CH_091105
         (633 letters)



>FitnessBrowser__psRCH2:GFF1660
          Length = 464

 Score =  221 bits (562), Expect = 7e-62
 Identities = 144/445 (32%), Positives = 229/445 (51%), Gaps = 20/445 (4%)

Query: 107 ANTGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILY 166
           A T H + SL++ ++ RH+ +IALG  IGTGL +G+   L  AGP+ +++GYAI G I +
Sbjct: 3   AETLH-TGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPS-MILGYAIGGFIAF 60

Query: 167 CIIQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIK 226
            I++  GEM +V   + G ++ +         GF   W Y + ++ V   EL      ++
Sbjct: 61  LIMRQLGEM-IVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQ 119

Query: 227 YWTTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGA 286
           +W   V        F+VL+  IN+   + + E EF+F   K+  + G  +LG+ + V G 
Sbjct: 120 FWWPEVPTWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGK 179

Query: 287 GNDGFIGGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKA 345
           G +       W   G F NG      F G+   L    F+FGG E + IT AE + P+  
Sbjct: 180 GGEQASISNLWSHGGFFPNG------FSGMLLALAIIMFSFGGLELVGITAAEAAEPKTV 233

Query: 346 IPGAAKQMIYRILFLFLATIILLGFLVPYNSDQL-LGSTGGGTKASPYVIAVASHGVRVV 404
           IP A  Q++YRIL  ++  + +L  L P+++  L LG+ G     SP+V   +  G    
Sbjct: 234 IPKAINQVVYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTA 293

Query: 405 PHFINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFA 464
            H +N V+L + LS+ NS  Y ++R+   L+EQG AP+    I+  G P++A+GVSAL  
Sbjct: 294 AHLLNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVT 353

Query: 465 VIAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQT 524
           ++         +     L++++  + +  W  I L+HL+FRRAM+ QG    E  FK+  
Sbjct: 354 LLCVAVNYLFPQGALELLMSLAVAALVINWAMISLAHLKFRRAMQQQG---VEPSFKA-- 408

Query: 525 GVWG--SAYACIMMIL-ILIAQFWV 546
             W   S Y C+  +  ILI   W+
Sbjct: 409 -FWFPLSNYLCLAFVAGILIIMLWL 432


Lambda     K      H
   0.324    0.138    0.424 

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: 666
Number of extensions: 29
Number of successful extensions: 6
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: 633
Length of database: 464
Length adjustment: 35
Effective length of query: 598
Effective length of database: 429
Effective search space:   256542
Effective search space used:   256542
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 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