Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate BPHYT_RS20835 BPHYT_RS20835 pyridoxal 4-dehydrogenase
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >FitnessBrowser__BFirm:BPHYT_RS20835 Length = 338 Score = 321 bits (822), Expect = 2e-92 Identities = 162/333 (48%), Positives = 211/333 (63%), Gaps = 1/333 (0%) Query: 12 RRRIGRGPLQVTGLGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAE 71 +R+ R L+ T +G G AP+G ++R +S+E++ A I AAWDAGVRYFDTAP YG+ +E Sbjct: 6 KRKWPRSGLETTLMGFGAAPIGNIFRPISEEDSAALIKAAWDAGVRYFDTAPMYGHGLSE 65 Query: 72 HRLGDALRRYPRADYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSFE 131 R G ALR YPR +VLSTKVGR PR + W + LPF+ +DY++DG++RS E Sbjct: 66 ARCGQALRWYPRDQFVLSTKVGRLLKPRKRAEINFTPWVDGLPFDMRFDYSYDGVMRSIE 125 Query: 132 DSQQRLGIVDIDILLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGV 191 DS QR+ + IDI L+HDI THGD P + G +AL LR G +KAVG+GV Sbjct: 126 DSLQRMALEHIDIALIHDIDLFTHGDGQPQVFEAAMNGAA-KALLKLRDEGVVKAVGVGV 184 Query: 192 NEGAAILDAMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILARG 251 NE +A+ D DC LLAGRYTLLEQ LD LP CE+R VS++LGG +NSGILA G Sbjct: 185 NEWQVAHEAIRRSDFDCLLLAGRYTLLEQDALDGFLPLCEERQVSVVLGGGYNSGILATG 244 Query: 252 VQGDLKFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADE 311 K+NY AP ++ERV ++E VCR VPL AA+LQF HP + T + G RS + Sbjct: 245 AVPGAKYNYAPAPEAILERVRKIEQVCRDFSVPLKAASLQFVLGHPAIPTNIPGVRSVAQ 304 Query: 312 LRENAASFELPIPAALWFALREEGLLDSRAPAP 344 L +N +F IPA W L+ GL+ +P P Sbjct: 305 LEDNLQTFRADIPAEFWAELKRRGLIREDSPTP 337 Lambda K H 0.320 0.139 0.421 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: 304 Number of extensions: 9 Number of successful extensions: 2 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: 346 Length of database: 338 Length adjustment: 29 Effective length of query: 317 Effective length of database: 309 Effective search space: 97953 Effective search space used: 97953 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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