GapMind for catabolism of small carbon sources

 

Aligments for a candidate for antA in Pseudomonas fluorescens GW456-L13

Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate PfGW456L13_3819 Benzoate 1,2-dioxygenase alpha subunit (EC 1.14.12.10)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740
         (461 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3819 Benzoate
           1,2-dioxygenase alpha subunit (EC 1.14.12.10)
          Length = 454

 Score =  413 bits (1062), Expect = e-120
 Identities = 215/452 (47%), Positives = 295/452 (65%), Gaps = 15/452 (3%)

Query: 12  EYIQGCLDFRPAEGIYRVARDMFTEPELFDLEMELIFEKNWIYACHESEIANPNDFLTMR 71
           EY+   L+  P +G+YR  R+MFT+P LFDLEME IFE NW+Y  HES+I N NDF T  
Sbjct: 6   EYLHSLLEDDPEQGLYRCKREMFTDPRLFDLEMEHIFEGNWLYLAHESQIPNINDFYTTT 65

Query: 72  AGRQPMIITRDGNNQLHALINACQHRGATLTRVSKGNQSTFTCPFHAWCYKSDGRLVKVK 131
            GRQ + I R+ +  L+A INAC HRGATL R   GN+S++TCPFH W + + G+L+KVK
Sbjct: 66  MGRQSIFIARNKDGVLNAFINACSHRGATLCRHKSGNKSSYTCPFHGWTFNNSGKLLKVK 125

Query: 132 APGE--YPEGFD-KATRGLKK-ARIESYKGFVFISLDVNGSDSLEDYLGDAKVFFDMMVA 187
            P    YP  F+ + +  L K AR ESY+GF+F SL  +    +E +LG++    DM+V 
Sbjct: 126 DPANAGYPSSFNCEGSHDLTKVARFESYRGFLFGSLKADVLPLVE-HLGESAKIIDMIVD 184

Query: 188 QSPTGELEILPGKSTYSYDGNWKLQHENGLDGYHVSTVHYNYVSTVQHRQQVNAANGGVS 247
           QS  G LE+L G S+Y Y+GNWKL  ENG DGYHVS+VH+NY +T   R+Q  A  G  +
Sbjct: 185 QSADG-LEVLRGSSSYIYEGNWKLTAENGADGYHVSSVHWNYAATQNQRKQREA--GDTN 241

Query: 248 DTLDYSKLGAGD-AETDDGWFSFKNGHSLLFSDMPNPTVRAGYATVMPRLIEEYGQQQAE 306
            T+      AG  A+   G++SF  GH LL++   NP  R  Y      L +++G+ +A+
Sbjct: 242 PTMS-----AGSWAKQGGGFYSFDKGHMLLWTRWANPEDRPLYER-RDELAQDFGKARAD 295

Query: 307 WMMHRLRNLNIYPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGVKGESDADRENRIRQF 366
           WM+   RNL +YP+++ MDQ SSQ+RI RP++ N+TEIT  CI  KGESD  R +RIRQ+
Sbjct: 296 WMIENSRNLCLYPNVYLMDQFSSQIRIARPISVNRTEITIYCIAPKGESDHARSSRIRQY 355

Query: 367 EDFFNVSGMGTPDDLVEFREAQRGFQARLERWNEVSRGSEKWVEGPTPNSEVLGINPVLT 426
           EDFFNVSGM TPDDL EFR  Q  +Q  +  WN++SRG+E W+EG    ++ + ++P+L+
Sbjct: 356 EDFFNVSGMATPDDLEEFRSCQTSYQGSVTTWNDMSRGAEHWIEGADEAAKEIDLHPLLS 415

Query: 427 GTEFTHEGLYINQHGSWQRFLLQGLEQKALKL 458
           G     EGL++ QH  WQ+ +L+ L  +  KL
Sbjct: 416 GVRTEDEGLFVLQHKYWQQTMLKALAAEQSKL 447


Lambda     K      H
   0.318    0.135    0.415 

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: 606
Number of extensions: 21
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: 461
Length of database: 454
Length adjustment: 33
Effective length of query: 428
Effective length of database: 421
Effective search space:   180188
Effective search space used:   180188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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 paper from 2022 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