Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate WP_058930069.1 AU252_RS06790 globin domain-containing protein
Query= CharProtDB::CH_003330 (396 letters) >NCBI__GCF_001484605.1:WP_058930069.1 Length = 386 Score = 202 bits (514), Expect = 1e-56 Identities = 135/400 (33%), Positives = 212/400 (53%), Gaps = 28/400 (7%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKE-IFNMSNQRNGDQREALFN 59 ML ++ ++AT+PL+ +T FY R+F +PEL + +F+ SNQR+G+Q++AL Sbjct: 1 MLSDKSRPVIEATLPLVGSRIGAITPKFYARLFAAHPELLDGLFSRSNQRSGNQQQALAG 60 Query: 60 AIAAYASNIENLPALLP--AVEKIAQKHTSFQIKPEQYNIVGEHLLAT----LDEMFSPG 113 +IAA+A+++ N P LP + +IA +H S I QY +V EHL A L E+ +P Sbjct: 61 SIAAFATHLVNNPGTLPETVLSRIAHRHASLGITEPQYQVVYEHLFAAIAEDLAEVITP- 119 Query: 114 QEVLDAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELE 173 E+ +AW + Y ++A+ I E +Y A++A G T +++ AK P +F LE Sbjct: 120 -EIAEAWTEVYWLMADALIKLEKGLY---AAQANGKMWT-PWKVAAKIPAGIGSMTFTLE 174 Query: 174 PVDGGAVAEYRPGQYLGVWLK-PEGFPHQEIRQYSLTRKPDGKGYRIAVKREEGGQVSNW 232 P D V PGQY+ V ++ P+G +++RQYSL+ G K ++GG+VS Sbjct: 175 PADDTPVTAALPGQYVSVKVQLPDGL--RQVRQYSLSGDA-GTSRSFTTKLDDGGEVSPV 231 Query: 233 LHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNW 292 LHN VGD++++ P G+ + D PV L SAG+G TP ++L +LA++G QV Sbjct: 232 LHNTVEVGDILEISNPYGEITLKDGDG-PVVLASAGIGCTPTASILRSLAESGSDRQVLV 290 Query: 293 FHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAF 352 HA D A ++ + + L W +P +EG M L +++ Sbjct: 291 LHAESTLDSWALRGQMTDDVERLADADLQLWLEEPRAG-------ANEGFMSLREVD--- 340 Query: 353 SDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 YLCGP+ FM+ + + G+ IHYE FGP Sbjct: 341 LPANASLYLCGPLPFMKHIRNEAISAGIPATRIHYEVFGP 380 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: 380 Number of extensions: 22 Number of successful extensions: 8 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: 386 Length adjustment: 31 Effective length of query: 365 Effective length of database: 355 Effective search space: 129575 Effective search space used: 129575 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 Apr 09 2024. 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