Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate Pf1N1B4_5798 2-chlorobenzoate 1,2-dioxygenase reductase component
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5798 Length = 337 Score = 279 bits (713), Expect = 8e-80 Identities = 146/338 (43%), Positives = 208/338 (61%), Gaps = 8/338 (2%) Query: 1 MNHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYS-- 58 M H +AF+F DG T F A E + DAA R GI IPLDCR+G CGTC+ E+G Y Sbjct: 1 MTHSIAFNFEDGVTRFIDANAGETVADAAYRQGINIPLDCRDGACGTCKCFAEAGRYDLG 60 Query: 59 QDYVDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVS 118 +DY+ E+ALS+ + QQ +L+CQ R +SD S +C T+SAV Q+S Sbjct: 61 EDYI-EDALSADEAQQGFVLTCQMRAQSDCVVRVPVSSDVCRTR-QASYDATISAVRQLS 118 Query: 119 ASTAILQVQLDQA--LDFLPGQYARLSVPGTDSWRSYSFANLPGN-HLQFLVRLLPDGVM 175 ST L ++ + L FLPGQY L VPG++ R+YSF++L + + FL+R +P G+M Sbjct: 119 DSTIALSIKGESLSKLAFLPGQYVNLGVPGSEQTRAYSFSSLQRDGEVSFLIRNVPGGLM 178 Query: 176 SNYLRERCQVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPV 235 S++L + GD + + PLG+FYLR + +PL+L+AGGTGL+ ML+++A G E P+ Sbjct: 179 SSFLTGMAKAGDSMSLAGPLGSFYLRDIRRPLLLLAGGTGLAPFTAMLEKIAEQGSEHPL 238 Query: 236 HLYYGVRGAEDLCEAARIRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAELRDG 295 HL YGV DL E R+ A+AA+I N ++ ++ P K GY+T+H + L +G Sbjct: 239 HLIYGVTNDFDLVELDRLEAFAARIANFSFSACVANPDSRHPLK-GYVTQHIEPRHLNEG 297 Query: 296 SADMYLCGPPPMVESIQQWLADQALDGVQLYYEKFTQS 333 D+YLCGPPPMVE++ Q++ DQ + YYEKF S Sbjct: 298 DVDVYLCGPPPMVEAVSQFIRDQGIAPANFYYEKFAAS 335 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: 341 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: 335 Length of database: 337 Length adjustment: 28 Effective length of query: 307 Effective length of database: 309 Effective search space: 94863 Effective search space used: 94863 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