Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate PfGW456L13_4938 Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12.17)
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4938 Length = 393 Score = 264 bits (675), Expect = 3e-75 Identities = 161/401 (40%), Positives = 218/401 (54%), Gaps = 14/401 (3%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 ML AQ A VK+T+PLL G L HFY M + P+++ +FN ++Q +GDQ AL N Sbjct: 1 MLSAQDRAIVKSTVPLLESGGEALITHFYRMMLSEYPQVRPLFNQAHQASGDQPRALANG 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFS---PGQEVL 117 + YA +I+ L L V KI KH + QI PE Y IVG LL + E+ EV+ Sbjct: 61 VLMYARHIDQLDQLGDLVAKIINKHVALQILPEHYPIVGSCLLRAIAEVLGEEIATPEVI 120 Query: 118 DAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDG 177 AWG AYG LA++ I E IY++ GGW G R+F + K SA ITSF EP D Sbjct: 121 AAWGAAYGQLADILIGAETSIYDQKEQAPGGWRGAREFIVADKVEESAEITSFYFEPADK 180 Query: 178 GAVAEYRPGQYLGVWLKPEGFPHQEIRQ-YSLTRKPDGKGYRIAVKREEGGQVSNWLHNH 236 G + PGQY+G+ L +G +EIR+ YSL+ + YRI+VKRE GG+ SN+LH+ Sbjct: 181 GPILLAEPGQYIGMKLILDG---EEIRRNYSLSALANKGQYRISVKREAGGRASNFLHDQ 237 Query: 237 ANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAA 296 +VG ++L P+G+F + A D P+ LIS GVG TP LAML+ + V++ H A Sbjct: 238 LHVGASIQLFPPSGEFVL-TASDKPLVLISGGVGITPTLAMLEAALET--QRPVHFIHCA 294 Query: 297 ENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKL-EGAFSDP 355 NG VHAF D + L + P+ Y SE D GL+ +L + + Sbjct: 295 RNGSVHAFRDWIDGLAERHPQLKRFYCY---SEDDGVSPAAHKMGLLSQQQLHQWLPQER 351 Query: 356 TMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396 + Y GP GFM + L LGV ++ YE FGP L Sbjct: 352 DLDAYFLGPKGFMVAIKRHLKALGVPEKQSRYEFFGPAAAL 392 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: 397 Number of extensions: 27 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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