Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate RR42_RS26425 RR42_RS26425 biphenyl 2,3-dioxygenase
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS26425 Length = 429 Score = 360 bits (924), Expect = e-104 Identities = 179/407 (43%), Positives = 261/407 (64%), Gaps = 5/407 (1%) Query: 21 FPHDDGSRVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVV 80 +P D +P V++S AVYD E E+IFRG +WNFVALEAEIPN GDFK ++VG TPVVV Sbjct: 24 WPEDALHFIPDWVYTSNAVYDLELEKIFRGRSWNFVALEAEIPNPGDFKRSYVGPTPVVV 83 Query: 81 TRTEDGALSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGM 140 R EDG+++ + NRCAHRGA+ CR +GNA C YHQWS+D +GNL GVPF+RG Sbjct: 84 ARAEDGSVNVFENRCAHRGAEFCRHGQGNAKEFVCPYHQWSYDLKGNLQGVPFKRGVNRA 143 Query: 141 TGMPADFDPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFH-KPIEY 199 GMP DF + HGL KL V + G++FA++++D+ PL Y+ ++ D +F+ KP++ Sbjct: 144 GGMPKDFRNEDHGLVKLNVATRNGVIFASYANDMEPLDVYMTPEILKDFDVVFNGKPLKI 203 Query: 200 LGCTRQYSKSNWKLYMENVKDPYHASMLHLFHTTFNIFRVGMKARSIPDANHGLHSIITV 259 LG + NWK+Y EN+KDPYHA++LH F F + G + I D HG H + Sbjct: 204 LGYYKNELPCNWKMYHENLKDPYHATLLHSFLVVFGLLVAGNDSAMIADPVHGRHGTMAS 263 Query: 260 TKTGDDTSAAYKQQN---IRSFDEGFHLEDESILDLVSEYDEDCTNHIQPIFPQLVIQQI 316 K +D AA +N +RS+ EG L+D+ L+ + E+D + +Q I+P L++Q+ Sbjct: 264 AKK-EDKYAAVSDENKKEMRSYHEGMRLQDDRFLEYIKEFDSPWSVTMQTIWPNLIVQRE 322 Query: 317 HNTLVARQILPKGPDNFELIFHFFGYADDTPELRALRIKQANLVGPAGYISMEDTEATEL 376 NTL RQI+P GPD+ + + FGY DDT E+ R++Q NL+GPAG++ +ED EA + Sbjct: 323 MNTLGVRQIVPNGPDSMLMQWTMFGYEDDTEEMTRHRLRQGNLMGPAGFLGLEDNEAMKF 382 Query: 377 VQRGTVRDADATSVIEMSRGNPEQQDTVITESLIRKFWVGYQKLMGY 423 VQ G R + +V+++ G+ +++I+ES IR + Y+ +MG+ Sbjct: 383 VQEGVRRSSTERNVLKLDPGHVGTANSLISESAIRAMYQYYRSVMGF 429 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: 574 Number of extensions: 30 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: 423 Length of database: 429 Length adjustment: 32 Effective length of query: 391 Effective length of database: 397 Effective search space: 155227 Effective search space used: 155227 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