Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate RR42_RS27360 RR42_RS27360 CDP-6-deoxy-delta-3,4-glucoseen reductase
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__Cup4G11:RR42_RS27360 Length = 332 Score = 148 bits (374), Expect = 2e-40 Identities = 107/320 (33%), Positives = 163/320 (50%), Gaps = 10/320 (3%) Query: 17 FPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYSQDYVDEEALSSLDLQQRK 76 F V A+E +LD ALR +++ DCR G C TC+ R G + D L+ + + Sbjct: 14 FDVDADESVLDGALRANVQMAHDCRFGGCATCRVRLVEGAVAYDEYPM-GLTPEEEAEGF 72 Query: 77 MLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVSASTAILQVQLDQA--LDF 134 L+CQ R SD C P + + + +SA L ++L QA LD+ Sbjct: 73 ALACQARPTSDLVISTARPGEPCAEPA--RHTAVIRKIAPLSADVVHLTLELPQAPALDY 130 Query: 135 LPGQYARLSVPGTDSWRSYSFANLPGNHLQFL-VRLLPDGVMSNYLRERCQVGDELLMEA 193 PGQY ++ G RS+S A++P + L VR +P G + L + D+L +E Sbjct: 131 RPGQYLKIFT-GDGIARSFSMASVPRDRTVDLHVRRIPGGYFTERLLAGLRSDDQLDVEL 189 Query: 194 PLGAFYLRHVT-QPLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRGAEDLCEAAR 252 PLG FY R +PLV+VA GTGL+ + +L+ L + PV LY+G+R DL + Sbjct: 190 PLGGFYFRKDDYRPLVMVATGTGLAPIKSILESLMDDPDCPPVSLYWGMRTQADLYLHEQ 249 Query: 253 IRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAELRDGSAD-MYLCGPPPMVESI 311 I+A+ A++ + +Y VLS WSG+RG++ +H A+L D S +YLCG P M+ Sbjct: 250 IQAWGARLYDFQYVPVLSRADGAWSGRRGHV-QHAVAADLPDLSEHAIYLCGSPDMICDA 308 Query: 312 QQWLADQALDGVQLYYEKFT 331 ++ G +Y + FT Sbjct: 309 RETFLGLGASGAHIYADSFT 328 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: 332 Number of extensions: 22 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: 335 Length of database: 332 Length adjustment: 28 Effective length of query: 307 Effective length of database: 304 Effective search space: 93328 Effective search space used: 93328 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