Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate YP_004141784.1 Mesci_2598 oxidoreductase FAD/NAD(P)-binding domain-containing protein
Query= CharProtDB::CH_003330 (396 letters) >NCBI__GCF_000185905.1:YP_004141784.1 Length = 375 Score = 185 bits (470), Expect = 2e-51 Identities = 111/257 (43%), Positives = 144/257 (56%), Gaps = 12/257 (4%) Query: 151 GTRDFRIVAKTPRSALITSFELEPVDGGAVAEYRPGQYL----GVWLKPEGFPHQEIRQY 206 G RD ++VAK SALITSF +EPVD +++PGQ+L V + G +R Y Sbjct: 14 GFRDLKVVAKVRESALITSFHIEPVDPQDWRDFQPGQFLVFRIPVAREAAGERGYVLRNY 73 Query: 207 SLTRKPDGKGYRIAVKREEG-------GQVSNWLHNHANVGDVVKLVAPAGDFFMAVADD 259 S++ PD YRI+VKRE G S +LH+ +VGDV++ P GDF + A + Sbjct: 74 SISCSPDSASYRISVKREAAPGPGLPDGISSCFLHDRIDVGDVLQAEGPRGDFVLYKASN 133 Query: 260 TPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAAENGDVHAFADEVKELGQSLPRFT 319 PV L+S GVG TPM++ML LA V + HA +NGDVHA DEV L + P T Sbjct: 134 RPVVLLSGGVGLTPMVSMLHALASLPDRRAV-FIHACDNGDVHALRDEVSGLVSTRPGLT 192 Query: 320 AHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLG 379 AH YR PSE D+A+ +F SEG++ L+ FYLCGP FMQ L +LG Sbjct: 193 AHFCYRHPSERDKAEQRFHSEGMISRDVLQRLLPIDDYDFYLCGPPPFMQAIYVMLRELG 252 Query: 380 VKQENIHYECFGPHKVL 396 + I YE FGP VL Sbjct: 253 APRYRIAYEFFGPATVL 269 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: 373 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 396 Length of database: 375 Length adjustment: 30 Effective length of query: 366 Effective length of database: 345 Effective search space: 126270 Effective search space used: 126270 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 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