Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate RR42_RS34595 RR42_RS34595 FAD-binding oxidoreductase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS34595 Length = 704 Score = 131 bits (329), Expect = 7e-35 Identities = 93/267 (34%), Positives = 127/267 (47%), Gaps = 21/267 (7%) Query: 135 EAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGGAVAEYRPGQYLGVWLK 194 EA A+ A W R FR+ S++I SF LEP DG + GQ+L + + Sbjct: 332 EAGSRQRAAALANAW---RPFRVARIVDESSVIRSFHLEPADGAGRVAHLAGQFLPIRVT 388 Query: 195 PEGFPHQEIRQYSLTRKPDGKGYRIAVKREEGGQVSNWLHNHANVGDVVKLVAPAGDFFM 254 G +R Y+L+ P YRI+VKRE G VS LH++ VGD+++ AP G F + Sbjct: 389 LAGQAQPVMRTYTLSVSPADDVYRISVKRE--GTVSRHLHDNVRVGDLIEARAPTGAFTI 446 Query: 255 AVADDTPVTLISAGVGQTPMLAMLDTLAKAG---HTAQVNW-FHAAENGDVHAFADEVKE 310 A+ P L++AG+G TPMLAML + G + W FH+A AF+ E+ Sbjct: 447 DAAERRPAVLLAAGIGVTPMLAMLRHIVYEGLRKRRVRPAWFFHSARTVAERAFSKELAT 506 Query: 311 LGQS------LPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDPTMQFYLCGP 364 L +S L R + P +A R K +D G +D+ L FYLCGP Sbjct: 507 LTESAGGAVELVRLLS-----DPKDATRVK-DYDVSGRIDIGLLRARLPLDDYDFYLCGP 560 Query: 365 VGFMQFTAKQLVDLGVKQENIHYECFG 391 FMQ L L + IH E FG Sbjct: 561 TAFMQSLYDGLRALNIADSRIHAEAFG 587 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: 630 Number of extensions: 26 Number of successful extensions: 3 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: 704 Length adjustment: 35 Effective length of query: 361 Effective length of database: 669 Effective search space: 241509 Effective search space used: 241509 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: 52 (24.6 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