Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate PP_0808 PP_0808 Flavohemoprotein
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Putida:PP_0808 Length = 392 Score = 291 bits (745), Expect = 2e-83 Identities = 170/400 (42%), Positives = 226/400 (56%), Gaps = 13/400 (3%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 ML+A+ A +KAT+PLL G LT HFY M + PE++ +FN ++Q +GDQ AL N Sbjct: 1 MLNAEQRAIIKATVPLLESGGEALTTHFYKMMLSEYPEVRPLFNQAHQASGDQPRALANG 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG---QEVL 117 + YA +I+ L L V +I KH + QI PE Y IVG LL ++E+ V+ Sbjct: 61 VLMYARHIDQLEQLGGLVGQIINKHVALQILPEHYPIVGSCLLRAIEEVLGKDIATPAVI 120 Query: 118 DAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDG 177 DAWG AYG LA++ I E +Y E GGW GTR+FR+V + S+ I SF PVDG Sbjct: 121 DAWGAAYGQLADILIGAEENLYKEKEEAEGGWRGTREFRLVRREQESSEIVSFYFAPVDG 180 Query: 178 GAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEGGQVSNWLHNHA 237 V + PGQY+G+ L +G ++ R YSL+ DGK YRI+VKRE GG+VSN+LH+ Sbjct: 181 MPVLKAEPGQYIGLKLDIDG--AEQRRNYSLSALCDGKEYRISVKREAGGKVSNYLHDEL 238 Query: 238 NVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAAE 297 VGD ++L PAGDF +A A D P+ LIS GVG TP LAML + +V++ H A Sbjct: 239 KVGDTLQLFPPAGDFTLA-ASDKPLVLISGGVGITPTLAMLQAALQT--RREVHFIHCAR 295 Query: 298 NGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKL-EGAFSDPT 356 NG VHAF D + L P+ Y +P A D+ GL+ L E + Sbjct: 296 NGAVHAFRDWIDGLAARHPQLKRFYCYAEPEGGAAA----DAVGLLSEDLLAEWLPQERD 351 Query: 357 MQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396 + Y GP GFM +QL LGV ++ YE FGP L Sbjct: 352 VDAYFLGPKGFMAAVKRQLKGLGVPEQQSRYEFFGPAAAL 391 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: 410 Number of extensions: 24 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: 392 Length adjustment: 31 Effective length of query: 365 Effective length of database: 361 Effective search space: 131765 Effective search space used: 131765 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