Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate H281DRAFT_03646 H281DRAFT_03646 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin reductase subunit
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Burk376:H281DRAFT_03646 Length = 421 Score = 233 bits (593), Expect = 1e-65 Identities = 154/399 (38%), Positives = 209/399 (52%), Gaps = 4/399 (1%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 V++G G AA + LR D +VMI E LPY+RP LSK L + + Sbjct: 23 VVIGGGQAAGWVVKTLRKEGFDGRLVMIADEVHLPYERPPLSKAVLSGEADIDTVRLVKP 82 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVVA 126 +D I +I+RE + VR G + Y +LV+ATG R + + Sbjct: 83 DDFDTLNIEAWQPDCATSIDREQRIVRTQSGREVQYDRLVIATGGAARRLPESLVSTSHI 142 Query: 127 HYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRALP 186 Y+RT+ +A AL +L RRV V+GGG+IGLEVAA AR+LG + TV++ A RL R+LP Sbjct: 143 AYLRTLDEAVALGERLRASRRVLVVGGGWIGLEVAATARKLGVDATVVEGAPRLCARSLP 202 Query: 187 EVVGAYAHRLHDERGVGFQM-ATLPRAIRAAAGGGAIVET--DRGDVHADVVVVGIGVLP 243 +V + +LH GV ++ A L + I T D + AD V GIG+ P Sbjct: 203 PMVSDFLLQLHRANGVDVRLSAALTKLEDHPNDANRIRATFADGSTLDADFAVAGIGLTP 262 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPA 303 + LA+AAG+ V +GI VD T D IFA G+V H + L R VR+ESW A+NQ Sbjct: 263 HTALAEAAGVKVQDGIVVDHFGATDDPRIFACGDVANHPSAWLKRRVRLESWANAQNQAI 322 Query: 304 VAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDG 363 A LLG + YA++PW WSDQYD NLQ+LG A VRGD A T+F L DG Sbjct: 323 ATAKALLGTFEPYADIPWFWSDQYDVNLQILGDIPADAQLAVRGDLAAKRATLFHL-EDG 381 Query: 364 RIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGL 402 I A+N R++ +R+ + G D L D + L Sbjct: 382 AIRGVIAINTPRELKLSRKWMNQGRTIDLATLTDASTAL 420 Lambda K H 0.322 0.138 0.410 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: 350 Number of extensions: 13 Number of successful extensions: 5 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: 406 Length of database: 421 Length adjustment: 31 Effective length of query: 375 Effective length of database: 390 Effective search space: 146250 Effective search space used: 146250 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 (21.9 bits) S2: 50 (23.9 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