Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate Echvi_4494 Echvi_4494 Hemoglobin-like flavoprotein
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Cola:Echvi_4494 Length = 402 Score = 257 bits (657), Expect = 4e-73 Identities = 147/401 (36%), Positives = 220/401 (54%), Gaps = 14/401 (3%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 M TI VK+T P+L E G ++T FY ++F +P+L+ +FNM+NQ G Q + L NA Sbjct: 1 MASKSTIEIVKSTAPVLKEYGEQITKVFYKKLFETHPDLRNLFNMTNQVKGTQPKVLANA 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118 I YA+ IE LL AV IA KH+S I PE Y IVGE LL + E+ +++ Sbjct: 61 IIQYATYIETPEVLLQAVNSIAHKHSSLSITPEMYPIVGETLLWAIKEVLGDAATPDIIG 120 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178 AW +AYG LA +FI +E IY E S+ G+ G ++F++V K + ITSF L DG Sbjct: 121 AWAEAYGELAEIFIAKEDSIYREQKSRMNGYNGQKEFKVVRKIEENKHITSFYLNTTDGS 180 Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG---GQVSNWLHN 235 + E+ PGQY+ + L G H R YSL+ + + RI+VKRE G G VSN+LH+ Sbjct: 181 GLPEFTPGQYISLTLSIPGTDHLHTRNYSLSDYGNKEALRISVKRESGKYKGLVSNYLHD 240 Query: 236 HANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHA 295 GD++ L P+G+F++ ++ P+ ++AGVG TP+++M +L G ++ + Sbjct: 241 QVGEGDILSLGMPSGEFYLN-SNKGPLVFLAAGVGITPLISMYKSL--KGSEREIVFVQC 297 Query: 296 AENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDP 355 A+N + HAF +E++ Q T+ Y +P D FD +G + L Sbjct: 298 AKNSESHAFRNEIE--SQKTDNVTSVVIYEEPLSND----IFDFKGYLTSKVLNDILPSS 351 Query: 356 TMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396 Y+CGP FM + L + K ++H+E FGP + L Sbjct: 352 PSDVYMCGPKSFMAYALDLLKEHEGKISDVHFEFFGPKEEL 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: 391 Number of extensions: 20 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: 402 Length adjustment: 31 Effective length of query: 365 Effective length of database: 371 Effective search space: 135415 Effective search space used: 135415 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