Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate Ac3H11_217 Ortho-halobenzoate 1,2-dioxygenase alpha-ISP protein OhbB
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_217 Length = 441 Score = 288 bits (736), Expect = 3e-82 Identities = 159/428 (37%), Positives = 237/428 (55%), Gaps = 28/428 (6%) Query: 19 VHFPHDDGSRVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPV 78 + + D SR+P++ ++ A+Y +E +R+F W +V LEAEIPNAGDFK T +G+ V Sbjct: 13 IRWETDGTSRIPFQAYTDEALYRKELDRLFYNGHWCYVGLEAEIPNAGDFKRTVIGERSV 72 Query: 79 VVTRTEDGALSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRG-- 136 ++ R +D ++ N CAHRG CR+ GN S TC YHQW++ G+L GVPFRRG Sbjct: 73 LLVRDKDASIHVVENVCAHRGMAFCRERHGNRESLTCPYHQWNYTLSGDLQGVPFRRGVK 132 Query: 137 QKGMT--GMPADFDPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFH 194 Q G GMPADF+P +HGL KL+V + G+VFA+F V PL ++LG + + DR+F+ Sbjct: 133 QDGKVNGGMPADFNPAEHGLTKLKVATRGGVVFASFDHSVEPLEEFLGPTILGYFDRLFN 192 Query: 195 -KPIEYLGCTRQYSKSNWKLYMENVKDPYHASMLHLFHTTFNIFRVGMKARSIPDANHGL 253 + + LG RQ NWKL EN+KDPYH +LH + TF ++R K++ + DA H Sbjct: 193 GRKLTILGYNRQRIPGNWKLMQENIKDPYHPGLLHTWFVTFGLWRADNKSQLLMDAQH-R 251 Query: 254 HSIITVTKTGDDTSAAYKQQNIRSFDEGFHLEDESILDLVSE----------YDEDC--- 300 H+ + T+ +A Q + SF G L D LD+ E E Sbjct: 252 HAAMVSTRGAAGKAADVTQ--VSSFKAGMELNDPRFLDIAQEGWWAGPAPAASGEGAAVP 309 Query: 301 -------TNHIQPIFPQLVIQQIHNTLVARQILPKGPDNFELIFHFFGYADDTPELRALR 353 T + +FP ++ QQ N++ R I P G F+ ++ FG+ DD+ E+ R Sbjct: 310 SAGAAVPTAVMMTVFPSVIFQQQVNSVSTRHIQPDGKGAFDFVWTHFGFEDDSEEMTQRR 369 Query: 354 IKQANLVGPAGYISMEDTEATELVQRGTVRDADATSVIEMSRGNPEQQDTVITESLIRKF 413 ++QANL GPAG++S +D E E Q G ++ E+ D ++TE+LIR Sbjct: 370 LRQANLFGPAGFVSADDGEVIEWSQEGFETKPAHRTLAELGGREVGDTDHMVTETLIRGM 429 Query: 414 WVGYQKLM 421 + ++K+M Sbjct: 430 YEYWRKVM 437 Lambda K H 0.321 0.136 0.420 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: 518 Number of extensions: 25 Number of successful extensions: 4 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: 423 Length of database: 441 Length adjustment: 32 Effective length of query: 391 Effective length of database: 409 Effective search space: 159919 Effective search space used: 159919 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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