Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate GFF1621 PS417_08245 CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3- dehydrase reductase
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__WCS417:GFF1621 Length = 329 Score = 114 bits (284), Expect = 4e-30 Identities = 106/352 (30%), Positives = 157/352 (44%), Gaps = 49/352 (13%) Query: 2 NHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYSQDY 61 NHK +F+ GK+L L+ A G + CR G CG C+ GD ++ Sbjct: 8 NHK-SFTGESGKSL----------LECAKSQGTVLEYSCRTGRCGVCKANVLQGD-TEVM 55 Query: 62 VDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGT---VSAVEQVS 118 E AL+ + +L+C +D + D +Q+K + +E+++ Sbjct: 56 QPELALTDEERANGAILTCCRAALTDV----ELDIEDLGLLADIQIKTMPCRLDTLERLA 111 Query: 119 ASTA--ILQVQLDQALDFLPGQYARLSVPGTDSWR-SYSFANLPGNH--LQFLVRLLPDG 173 +L+ AL +LPGQY + V G D R SYS AN L+ +R +PDG Sbjct: 112 DDVVRVVLRTPPKSALFYLPGQY--IDVIGKDGVRRSYSIANAVREDAKLELHIRQVPDG 169 Query: 174 VMSNYLRERCQVGDELLMEAPLGAFYLRHV-TQPLVLVAGGTGLSALLGMLDQLAANG-- 230 VMS Y QV D L +E PLG F LR+ T LV +A GTG++ + ML+ LA+ Sbjct: 170 VMSQYWFGEAQVNDLLRLEGPLGTFCLRNASTTNLVFMATGTGIAPVKAMLEALASTSEP 229 Query: 231 -CEQPVHLYYGVRGAEDLCEAARIRAYAAKIPNL--RYTEVLSAPSEEWSGKRGY----- 282 + V++Y+G R DL + P L Y VLS + W G GY Sbjct: 230 LIGKRVYVYWGGRTENDL-------YWLPDFPTLGMTYRPVLSRAGKHWPGATGYVQQAV 282 Query: 283 LTEHFDLAELRDGSADMYLCGPPPMVESIQQWLADQALDGVQLYYEKFTQSN 334 L E+ DLA+ +Y CG M+ + ++ L L + + F SN Sbjct: 283 LAENLDLAD-----TSVYACGSEAMIHTAREMLTQAGLPLKHFHSDAFVSSN 329 Lambda K H 0.320 0.136 0.412 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: 264 Number of extensions: 13 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: 335 Length of database: 329 Length adjustment: 28 Effective length of query: 307 Effective length of database: 301 Effective search space: 92407 Effective search space used: 92407 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