GapMind for catabolism of small carbon sources

 

Alignments for a candidate for antA in Pseudomonas putida KT2440

Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate PP_3161 PP_3161 benzoate 1,2-dioxygenase subunit alpha

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



>FitnessBrowser__Putida:PP_3161
          Length = 452

 Score =  407 bits (1047), Expect = e-118
 Identities = 214/456 (46%), Positives = 296/456 (64%), Gaps = 16/456 (3%)

Query: 12  EYIQGCLDFRPAEGIYRVARDMFTEPELFDLEMELIFEKNWIYACHESEIANPNDFLTMR 71
           +Y+   L+    +GIYR  R+MFT+P LFDLEM+ IFE NWIY  HES+I   NDFLT+ 
Sbjct: 6   DYLNAMLEDDREKGIYRCKREMFTDPRLFDLEMKHIFEGNWIYLAHESQIPEKNDFLTLT 65

Query: 72  AGRQPMIITRDGNNQLHALINACQHRGATLTRVSKGNQSTFTCPFHAWCYKSDGRLVKVK 131
            GRQP+ I R+ + +L+A +NAC HRGA L R  +GN+S++TCPFH W + + G+L+KVK
Sbjct: 66  MGRQPIFIARNKDGELNAFLNACSHRGAMLCRHKRGNRSSYTCPFHGWTFNNSGKLLKVK 125

Query: 132 APGE--YPEGF--DKATRGLKKARIESYKGFVFISLDVNGSDSLEDYLGDAKVFFDMMVA 187
            P    YP+ F  D +    K AR ESY+GF+F SL+ +    L ++LG++    DM+V 
Sbjct: 126 DPSNAGYPDSFNCDGSHDLTKVARFESYRGFLFGSLNAD-VKPLVEHLGESAKIIDMIVD 184

Query: 188 QSPTGELEILPGKSTYSYDGNWKLQHENGLDGYHVSTVHYNYVSTVQHRQQVNAANGGVS 247
           QSP G LE+L G S+Y Y+GNWKL  ENG DGYHVS+VH+NY +T   R+Q  A      
Sbjct: 185 QSPEG-LEVLRGASSYIYEGNWKLTAENGADGYHVSSVHWNYAATQNQRKQREA-----G 238

Query: 248 DTLDYSKLGAGDAETDDGWFSFKNGHSLLFSDMPNPTVRAGYATVMPRLIEEYGQQQAEW 307
           D +     GA  A+   G++SF +GH LL++   NP  R  Y     +L  ++GQ +A+W
Sbjct: 239 DEIKTMSAGAW-AKQGGGFYSFDHGHLLLWTRWANPEDRPAYER-RDQLAADFGQARADW 296

Query: 308 MMHRLRNLNIYPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGVKGESDADRENRIRQFE 367
           M+   RNL +YP+++ MDQ SSQ+R+ RP++ NKTEIT  CI  KGES   R  RIRQ+E
Sbjct: 297 MIENSRNLCLYPNVYLMDQFSSQIRVARPISVNKTEITIYCIAPKGESADARAKRIRQYE 356

Query: 368 DFFNVSGMGTPDDLVEFREAQRGFQARLERWNEVSRGSEKWVEGPTPNSEVLGINPVLTG 427
           DFFNVSGM TPDDL EFR  Q G+      WN++SRG++ WVEG    ++ + + P+L+G
Sbjct: 357 DFFNVSGMATPDDLEEFRSCQTGYGGG-TGWNDMSRGAKHWVEGADEAAKEIELEPLLSG 415

Query: 428 TEFTHEGLYINQHGSWQRFLLQGL--EQKALKLKEV 461
                EGL++ QH  WQ  ++Q L  EQ+ + ++ V
Sbjct: 416 VRTEDEGLFVLQHKYWQDTMIQALKDEQQLIPVEAV 451


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: 613
Number of extensions: 27
Number of successful extensions: 7
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: 452
Length adjustment: 33
Effective length of query: 428
Effective length of database: 419
Effective search space:   179332
Effective search space used:   179332
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