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.
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:
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