Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate SMa1191 SMa1191 nitric oxide dioxygenase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Smeli:SMa1191 Length = 403 Score = 342 bits (876), Expect = 1e-98 Identities = 178/399 (44%), Positives = 250/399 (62%), Gaps = 8/399 (2%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 ML +T VKAT P+L + G + HFY RMF +PELK IFNM++Q G+Q++AL A Sbjct: 1 MLTQKTKDIVKATAPVLAQHGYAIIQHFYKRMFQAHPELKNIFNMAHQERGEQQQALARA 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118 + AYA+NIEN +L ++ IA KH S ++PEQY IVGEHLLA++ E+ E++ Sbjct: 61 VYAYAANIENPESLSAVLKDIAHKHASLGVRPEQYPIVGEHLLASIKEVLGDAATDEIIS 120 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178 AW +AYG LA++ E+E+Y + +AGGW G R F + K P S +ITSF LEP DGG Sbjct: 121 AWAQAYGNLADILAGMESELYERSEERAGGWAGWRRFIVREKNPESDVITSFVLEPADGG 180 Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG-----GQVSNWL 233 VA++ PGQY V ++ +Q+IRQYSL+ P+G+ YRI+VKRE+G G VS+ L Sbjct: 181 PVADFEPGQYTSVAVQVPKLGYQQIRQYSLSDSPNGRSYRISVKREDGGLGTPGYVSSLL 240 Query: 234 HNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWF 293 H+ NVGD +KL AP G+F++ V+ TP+ LIS GVG TPM++ML A +V + Sbjct: 241 HDEINVGDELKLAAPYGNFYIDVSATTPIVLISGGVGLTPMVSMLKK-ALQTPPRKVVFV 299 Query: 294 HAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFS 353 H A N VHA D +KE ++ P F +Y +P D +D GL+D+ K++ + Sbjct: 300 HGARNSAVHAMRDRLKEASRTYPDFKLFIFYDEPLPTDIEGRDYDFAGLVDVEKVKDSIL 359 Query: 354 DPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 +Y+CGPV FM+ +L+ LG+ + IHYE FGP Sbjct: 360 LDDADYYICGPVPFMRMQHDKLLGLGITEARIHYEVFGP 398 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: 410 Number of extensions: 17 Number of successful extensions: 4 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: 403 Length adjustment: 31 Effective length of query: 365 Effective length of database: 372 Effective search space: 135780 Effective search space used: 135780 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