Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate HSERO_RS06550 HSERO_RS06550 benzoate 1,2-dioxygenase subunit alpha
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740 (461 letters) >FitnessBrowser__HerbieS:HSERO_RS06550 Length = 462 Score = 395 bits (1014), Expect = e-114 Identities = 207/463 (44%), Positives = 298/463 (64%), Gaps = 24/463 (5%) Query: 1 MNSAKSITQWQEY---IQGCLDFRPAEGIYRVARDMFTEPELFDLEMELIFEKNWIYACH 57 MN+ + ++ E +Q L G++R RD+FT P+LF+LEM+ +FE NW+Y H Sbjct: 1 MNTTAAADRYDELDTLLQSALQEDKDNGVFRCRRDIFTNPDLFELEMKHLFESNWVYLAH 60 Query: 58 ESEIANPNDFLTMRAGRQPMIITRDGNNQLHALINACQHRGATLTRVSKGNQSTFTCPFH 117 ES+I ND+ T GRQP++ITRD + QL+A+INAC H+GA L R GN+S+FTCPFH Sbjct: 61 ESQIPEINDYYTTWIGRQPVVITRDKSGQLNAVINACSHKGAMLCRRKHGNKSSFTCPFH 120 Query: 118 AWCYKSDGRLVKVK--APGEYPEGFDK-ATRGLKK-ARIESYKGFVFISLDVNGSDSLED 173 W + + G+L+KVK EYP F+K + L + AR +SY+GF+F SL + LE+ Sbjct: 121 GWTFSNSGKLLKVKDEKTTEYPVSFNKNGSHDLTRVARFQSYRGFLFGSLSEDVLP-LEE 179 Query: 174 YLGDAKVFFDMMVAQSPTGELEILPGKSTYSYDGNWKLQHENGLDGYHVSTVHYNYVSTV 233 YLG+ +V D +V Q+P G LE+L G S+Y YDGNWK+Q ENG DGYHVS+VH+NY +T+ Sbjct: 180 YLGETRVIIDQIVDQAPNG-LEVLRGNSSYLYDGNWKMQMENGCDGYHVSSVHWNYAATM 238 Query: 234 QHRQQVNAANGGV--SDTLDYSKLGAGDAETDDGWFSFKNGHSLLFSDMPNPTVRAGYAT 291 R++ GG +D ++SK AG + F+NGH LL+++ NP VR + Sbjct: 239 SRRKE-----GGTKATDANNWSKAVAGV-------YGFENGHILLWTNTLNPEVRPIW-N 285 Query: 292 VMPRLIEEYGQQQAEWMMHRLRNLNIYPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGV 351 L GQ +A+ ++ + RNL +YP++F MDQ +Q+R+ RP++ +KTEI+ C Sbjct: 286 QREELAARVGQARADTIVAQTRNLCLYPNVFLMDQFGTQIRVARPISVDKTEISIFCFAP 345 Query: 352 KGESDADRENRIRQFEDFFNVSGMGTPDDLVEFREAQRGFQARLERWNEVSRGSEKWVEG 411 KGES+ DR RIRQ+EDFFNVSGMGT DDL EFR Q G+ RWN++SRG+ W EG Sbjct: 346 KGESEEDRRVRIRQYEDFFNVSGMGTADDLEEFRACQAGYAGSAVRWNDMSRGAPLWKEG 405 Query: 412 PTPNSEVLGINPVLTGTEFTHEGLYINQHGSWQRFLLQGLEQK 454 P N+ +G++P L+G EGL++ QH W + + ++++ Sbjct: 406 PDENARKMGMHPKLSGERSEDEGLFVCQHHYWTEQMRKAVKKE 448 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: 621 Number of extensions: 24 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: 462 Length adjustment: 33 Effective length of query: 428 Effective length of database: 429 Effective search space: 183612 Effective search space used: 183612 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