Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate WP_009399900.1 BLS63_RS09965 naphthalene 1,2-dioxygenase reductase component
Query= reanno::WCS417:GFF4631 (335 letters) >NCBI__GCF_900100495.1:WP_009399900.1 Length = 328 Score = 141 bits (356), Expect = 2e-38 Identities = 99/329 (30%), Positives = 161/329 (48%), Gaps = 12/329 (3%) Query: 11 DGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYSQDYVDEEALSSL 70 + + L F GAN LL+ + + I C G CGTC RC D S ++ S Sbjct: 8 NNRRLPFDSGAN--LLEVLREHRVGISYSCMSGRCGTC--RCRVIDGSVISSAAKSGDSN 63 Query: 71 DLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVSASTAILQVQLDQ 130 +++ +L+CQ+ + S+ + P + +KG V AVE + ++++L + Sbjct: 64 RIEEHYVLACQSVLTSNCAIEIIDSDDIVTHPARI-IKGMVVAVESPTHDIRRIRIRLAK 122 Query: 131 ALDFLPGQYARLSVPGTDSWRSYSFANLPGNH-LQFLVRLLPDGVMSNYLRERCQVGDEL 189 +F PGQYA L + R YS A LP + ++F +R +P G ++ Y+ E + G + Sbjct: 123 PFEFSPGQYAMLQF-SPEHVRPYSMAGLPDDQEMEFHIRKVPGGRVTEYIFEHVREGTSI 181 Query: 190 LMEAPLGAFYLRHV-TQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRGAEDLC 248 + PLG YLR T P++ V GGTGL+ +L ++ +G P+HLY+GVR +DL Sbjct: 182 KLSGPLGTAYLRQAHTGPMLCVGGGTGLAPVLSIVRGALKSGMTNPIHLYFGVRSQQDLY 241 Query: 249 EAARIRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTE--HFDLAELRDGSADMYLCGPPP 306 +A R+ AA P L V++ + G +T+ D+ L A YLCG P Sbjct: 242 DADRLNQLAAIHPQLTVHTVIATGPINEGQRAGLITDLIEKDIPSLAGWRA--YLCGAPA 299 Query: 307 MVESIQQWLADQALDGVQLYYEKFTQSNI 335 MV+++ D + +Y + F S + Sbjct: 300 MVDALCTVAKDLGISPEHIYADAFYPSGV 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: 298 Number of extensions: 19 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: 328 Length adjustment: 28 Effective length of query: 307 Effective length of database: 300 Effective search space: 92100 Effective search space used: 92100 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 24 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