Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate H281DRAFT_01789 H281DRAFT_01789 MOSC domain-containing protein YiiM
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Burk376:H281DRAFT_01789 Length = 586 Score = 135 bits (339), Expect = 4e-36 Identities = 87/242 (35%), Positives = 116/242 (47%), Gaps = 6/242 (2%) Query: 151 GTRDFRIVAKTPRSALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTR 210 G R + A SA + SF L+ DG + PGQYL + L+P R YSL+ Sbjct: 237 GFRPLTVAAIDEESADVVSFTLKSADG-QLQPALPGQYLVLRLQPTADGPPLFRSYSLSG 295 Query: 211 KPDGKGYRIAVKREEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVG 270 + YRI+VK E G WL +H + GD + + +P G F + D P+ L+SAG+G Sbjct: 296 PLSAESYRISVKIEPNGLAGAWLRSHVHAGDTLDVSSPRGSFVLQPGDG-PIVLLSAGIG 354 Query: 271 QTPMLAMLDTLAKAGHTAQVNWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEA 330 TP+LAML L+ T QV W H A + H FA E + L +L ++ Y Sbjct: 355 ATPVLAMLHALSSQQSTRQVLWLHTARDRQHHPFAVEARRLMLALAHGRSYVSYSAAGPN 414 Query: 331 DRAKGQFDSEGLMDLSKLE--GAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYE 388 DR FD+ G + L G F D + YLCGP FM K L L + E IH E Sbjct: 415 DRLGEDFDATGRLSQQILSEVGVFRDADV--YLCGPAPFMADMKKALAALEIAPERIHAE 472 Query: 389 CF 390 F Sbjct: 473 TF 474 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: 542 Number of extensions: 28 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: 586 Length adjustment: 34 Effective length of query: 362 Effective length of database: 552 Effective search space: 199824 Effective search space used: 199824 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: 51 (24.3 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