Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate GFF3014 HP15_2958 extracellular solute-binding protein family 1
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__Marino:GFF3014 Length = 416 Score = 255 bits (652), Expect = 1e-72 Identities = 156/413 (37%), Positives = 214/413 (51%), Gaps = 15/413 (3%) Query: 6 LAAALGATAALPFGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSGG 65 L AA + A LP A A ++EV HWWT+GGEA A L + + G+ W D A+AG GG Sbjct: 10 LTAAAVSAALLPAQALQAGEVEVLHWWTAGGEARAAVALKEMMEDQGHTWKDFAVAGGGG 69 Query: 66 -TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSLLD 124 A ++ +R G+P AA Q G E + G + L D+A NW +++ P + D Sbjct: 70 EAAMTVLKTRAVSGNPPAAAQIK-GLDIREWAKLGFLTSLDDVAEANNWGQLIPPV-IAD 127 Query: 125 SCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEKAGIVPLAVG 184 E PVN+H WLW + + GV VPK DEF AA L+ AGI PLA G Sbjct: 128 VMQYEDSYVAVPVNVHRVNWLWANPETLNKVGVGVPKTLDEFYQAAEKLKAAGITPLAHG 187 Query: 185 GQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARRMS---KGT 241 GQPWQ F+ + +A+ G ++F F + D +V ++ +VF A+ A+ MS Sbjct: 188 GQPWQDATVFEAVALAVMGPDDFASAFVEHDMDVINSAQMEEVF--AEFAKVMSYVDDNA 245 Query: 242 NVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDAF 301 +DWN AT MVI G+A QIMGDWA+GEF AG G DY C G + D+F Sbjct: 246 AGRDWNTATGMVIRGEAAMQIMGDWAKGEFTAAGLTPGEDYVCAAAPGTGGQFTFNVDSF 305 Query: 302 YFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLA--AANDCMKKGLDI 359 L DE+ +KAQ+ LA T+++PE Q FN KGS+PVR D D A+ D K + Sbjct: 306 AMFSLSDEDNTKAQKDLARTIMEPEFQAVFNKAKGSIPVRTDFDTCAQASMDTFKSSAE- 364 Query: 360 LAKGNVIQGTDQLLSADS--QKQKEDLFSEFFANHSMTPEDAQKRFADIIAAA 410 G ++ L+ S Q Q D+ + F + + P A + A I AA Sbjct: 365 --DGGLVPSFAHGLATTSYVQGQIFDVVTNFVNSDNKDPARATDQLAAAIQAA 415 Lambda K H 0.315 0.131 0.389 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: 512 Number of extensions: 23 Number of successful extensions: 5 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: 411 Length of database: 416 Length adjustment: 31 Effective length of query: 380 Effective length of database: 385 Effective search space: 146300 Effective search space used: 146300 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 (21.6 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