GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3819
          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:

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