Align Anthranilate 1,2-dioxygenase electron transfer component; EC 1.18.1.3 (characterized)
to candidate GFF2645 Psest_2697 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases
Query= SwissProt::O85675 (343 letters) >FitnessBrowser__psRCH2:GFF2645 Length = 336 Score = 284 bits (726), Expect = 3e-81 Identities = 148/340 (43%), Positives = 214/340 (62%), Gaps = 7/340 (2%) Query: 1 MNHSVALNFADGKTFFIAVQEDELLLDAAVRQGINLPLDCREGVCGTCQGTCETGIYE-- 58 M+H +ALNF DG T FI + E + DAA RQGIN+PLDCR+G CG C+ E G Y+ Sbjct: 1 MSHKIALNFEDGVTRFIDAKIGETVADAAYRQGINIPLDCRDGACGACKCFAEAGQYDLG 60 Query: 59 QEYVDEDALSERDLAKRKMLACQTRVKSNAAFYFDHHSSICNAGETLKIATVVTGVELVS 118 +EY+ EDALSE + A+ +L CQ R +S+ S +C + AT+ + V +S Sbjct: 61 EEYI-EDALSEDEAAQGYVLTCQMRAESDCVVRVPASSDVCKTAQASYEATI-SNVRQLS 118 Query: 119 ETTAILHLDASQHVKQLDFLPGQYARLQIPDTDDWRSYSFANRPNASNQLQFLIRLLPNG 178 ++T L + + + QL FLPGQY LQ+P TD R+YSF++ ++ FLIR +P G Sbjct: 119 QSTIALSIKG-EALTQLAFLPGQYVNLQVPGTDQTRAYSFSSLQR-DGEVSFLIRNVPGG 176 Query: 179 VMSNYLRERCQVGQTLIMEAPLGSFYLREVERPLVFIAGGTGLSAFLGMLDNIAEQPNQP 238 +MS++L + G +L + PLGSFYLRE++RPL+ +AGGTGL+ F ML+ IAEQ ++ Sbjct: 177 LMSSFLSGMAKAGDSLTLAGPLGSFYLREIKRPLLLLAGGTGLAPFTAMLEKIAEQGSEH 236 Query: 239 SVHLYYGVNTEADLCEQKRLTTYAERIKNFSYHPIISKASEQWQGKSGFIHEHLDKNQLS 298 +HL YGV+ + DL E RL +A RI NF+Y +S Q+ K G++ +H++ L+ Sbjct: 237 PLHLIYGVSNDFDLVEMDRLADFAARIPNFTYSACVSSTDSQYPQK-GYVTQHIEPKHLN 295 Query: 299 EQSFDMYLCGPPPMIEAVKTWLDEQAIADCHIYSEKFLQS 338 E D+YLCGPPPM+E+V ++ EQ + + Y EKF S Sbjct: 296 EGEVDIYLCGPPPMVESVNQFIREQGLQPANFYYEKFAAS 335 Lambda K H 0.319 0.134 0.401 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: 325 Number of extensions: 15 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: 343 Length of database: 336 Length adjustment: 28 Effective length of query: 315 Effective length of database: 308 Effective search space: 97020 Effective search space used: 97020 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: 49 (23.5 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