Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate HSERO_RS06560 HSERO_RS06560 NADH oxidase
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__HerbieS:HSERO_RS06560 Length = 351 Score = 249 bits (637), Expect = 6e-71 Identities = 136/336 (40%), Positives = 201/336 (59%), Gaps = 8/336 (2%) Query: 2 NHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESG--DYSQ 59 ++++A +F DG T GA E +LDAA RN I +P+DC +GVCGTC+ R ESG D Sbjct: 3 SYRIALNFEDGVTRIIDCGAKEKVLDAAFRNRINLPMDCSDGVCGTCKCRAESGLYDLGD 62 Query: 60 DYVDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVSA 119 DY+D+ ALSS + +L+CQ +SD S+ C G G V+ + + Sbjct: 63 DYIDD-ALSSDEAGAGMVLTCQMVPQSDCVIAVPVASTACKT-GTASFTGKVAGLSDLGG 120 Query: 120 STAILQVQLD-QALDFLPGQYARLSVPGTDSWRSYSFANLPG-NHLQFLVRLLPDGVMSN 177 + L ++ A FLPGQY + VPG+ RSYSF++ G + + FL++ +P G+MSN Sbjct: 121 AAFELVLEAPANAPAFLPGQYVNIGVPGSGQHRSYSFSSPSGASRMSFLIKNVPGGLMSN 180 Query: 178 YLRERCQVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHL 237 +L + G L + PLG+FYLR V +P++++AGGTGL+ L ML++LA G +QPVHL Sbjct: 181 WLAGASE-GATLELTGPLGSFYLRPVKRPVLMLAGGTGLAPFLSMLEELAQQGLDQPVHL 239 Query: 238 YYGVRGAEDLCEAARIRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAELRDGSA 297 YGV +DL R++A A ++P +T ++ P+ ++GY+T+H A L DG+ Sbjct: 240 IYGVTRDQDLVLVERLQALADRLPGFSFTTCVADPATT-HARQGYVTQHMPAAVLHDGNV 298 Query: 298 DMYLCGPPPMVESIQQWLADQALDGVQLYYEKFTQS 333 D+YLCGPPPMVE++Q+ + YYEKF S Sbjct: 299 DVYLCGPPPMVEAVQKHFQATGMQPASFYYEKFASS 334 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: 351 Number of extensions: 16 Number of successful extensions: 6 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: 351 Length adjustment: 29 Effective length of query: 306 Effective length of database: 322 Effective search space: 98532 Effective search space used: 98532 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