Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate H281DRAFT_04686 H281DRAFT_04686 nitric oxide dioxygenase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Burk376:H281DRAFT_04686 Length = 401 Score = 308 bits (790), Expect = 1e-88 Identities = 172/398 (43%), Positives = 223/398 (56%), Gaps = 13/398 (3%) Query: 2 LDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNAI 61 L A+ IA VKAT+P+L E G +T HFY RMF +PELK +FN ++Q++G+Q E L A+ Sbjct: 4 LTAEQIARVKATVPVLAEHGTTITKHFYKRMFARHPELKNLFNQTHQQSGNQPETLARAV 63 Query: 62 AAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLDA 119 AYA+NI+NL AL P V +IA KH S I+PE Y IVG HLL + ++ Q LDA Sbjct: 64 YAYAANIDNLGALGPTVSRIANKHASLNIRPEHYPIVGRHLLGAIVDVLGDAVDQPTLDA 123 Query: 120 WGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGGA 179 W AYG LAN+F+ EA++Y + W G R F++ K S ITSF L P DG A Sbjct: 124 WQVAYGQLANIFVGTEAKLY-----EGAAWSGFRPFKVARKQVESDEITSFYLTPADGSA 178 Query: 180 VAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG------GQVSNWL 233 ++ PGQY+ V + + RQYSL+ P GK RI+VKRE+G G VSN L Sbjct: 179 ACDFEPGQYVSVKRFVDKLGVDQPRQYSLSDAPHGKWLRISVKREDGREDIAPGHVSNLL 238 Query: 234 HNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWF 293 H G VV + AP GDF + TPV L+S GVG TPM +ML T+ G V + Sbjct: 239 HADVEEGTVVHVSAPMGDFTLDRKKTTPVVLMSGGVGVTPMTSMLSTILADGSERSVTFV 298 Query: 294 HAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFS 353 HA NG VHAF + E S +Y E DR +D +G +D++ + G Sbjct: 299 HACRNGRVHAFRQWLNETVASHSNVKRVVFYEAVGEGDRRGVDYDFDGRLDVAGIAGQVI 358 Query: 354 DPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFG 391 P +Y+CGPV FM+ L LGV IH E FG Sbjct: 359 VPDADYYICGPVPFMRAQCDALAALGVDPARIHTEVFG 396 Lambda K H 0.318 0.135 0.404 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: 413 Number of extensions: 20 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: 396 Length of database: 401 Length adjustment: 31 Effective length of query: 365 Effective length of database: 370 Effective search space: 135050 Effective search space used: 135050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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