Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate HSERO_RS06720 HSERO_RS06720 Rieske (2Fe-2S) protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740 (461 letters) >FitnessBrowser__HerbieS:HSERO_RS06720 Length = 428 Score = 214 bits (544), Expect = 6e-60 Identities = 131/394 (33%), Positives = 202/394 (51%), Gaps = 38/394 (9%) Query: 33 MFTEPELFDLEMELIFEKNWIYACHESEIANPNDFLTMRAGRQPMIITRDGNNQLHALIN 92 ++T+P LF+ EM+ IF K WI+ HESEI NP DF T + GRQP+I+ RD +++ L N Sbjct: 29 LYTDPALFEAEMDKIFYKTWIWVAHESEIKNPGDFKTAQIGRQPVIVVRDKTGKINVLEN 88 Query: 93 ACQHRGATLTRVSKGNQSTFTCPFHAWCYKSDGRLVKVKAPGEYPEGFDKATRGLKKARI 152 C+HRGAT+ KGN + FTCP+H+W Y DG+L + P Y + +KA L+ R Sbjct: 89 RCRHRGATVCEKHKGNATGFTCPYHSWSYGLDGKLRGLPYPEGYEDVIEKADLPLQSLRC 148 Query: 153 ESYKGFVFISLDVNGSDSLEDYLGDAKVFFDMMVAQSPTGELEILPGKSTYSYDGNWKLQ 212 ESY G +F S + + L D+LG AK + D+ + Q +++ G+ +S+ GNWK+Q Sbjct: 149 ESYHGMIFASFN-QEIEPLSDFLGHAKKWIDLFMKQGAGFPIKV-QGEHKFSFKGNWKIQ 206 Query: 213 HENGLDGYHVSTVHYNYVSTVQHRQQVNAANGGVSDTLDYSKLGAGDAETDDGWF--SFK 270 EN DGYH VH ++S+V S+ L + TDD S Sbjct: 207 LENTTDGYHFPVVHKTFLSSVDEE---------TSEMLSFM--------TDDQSITRSLG 249 Query: 271 NGHSLLFS---------DMPNPTVRAGYATVMPRLIEEYGQQQAEWMMHRLR----NLNI 317 NGHS++ D + ++ +A V L + +Q ++ L NLN+ Sbjct: 250 NGHSVMIMVPEHVDLDVDDGSEQLQERFAHVTEELSKTMPPEQVRRIVRSLHGAGFNLNL 309 Query: 318 YPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGVKGESDADRENRIRQFEDFFNVSGMGT 377 +P++ S R++ PV+ +T+I +G+ G + R+R E F G G+ Sbjct: 310 FPNVAMS---MSFFRVLHPVSVGETQIRHVALGMDGGPEIANRERLRIHEHFQGPFGFGS 366 Query: 378 PDDLVEFREAQRGFQARLERWNEVSRG-SEKWVE 410 PDD + Q G A + V+RG + +WV+ Sbjct: 367 PDDAEAWERVQAGSHAGRDAPILVNRGLNREWVD 400 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: 546 Number of extensions: 18 Number of successful extensions: 3 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: 428 Length adjustment: 32 Effective length of query: 429 Effective length of database: 396 Effective search space: 169884 Effective search space used: 169884 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