Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 294 bits (752), Expect = 6e-84 Identities = 178/487 (36%), Positives = 273/487 (56%), Gaps = 16/487 (3%) Query: 10 SSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG 69 S P++ A ++K FG AAL DV + GE HAL+G NGAGKSTL+ +L+G+ G Sbjct: 14 SDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEG 73 Query: 70 EVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGV-IDWQAMR 128 VR G RDA +A ++Q ++ +L VA+N+F+ R+ + G+ +D +A Sbjct: 74 AVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKASL 133 Query: 129 RDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188 AR LL+ I++ +AR G L V +QLVEIA+ALS AR +I+DEPT+ L E +R Sbjct: 134 EAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRR 193 Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248 LF+ + +L +GV ++ISH + EV ++ VTV RD RH+ + P++ L +I AM G Sbjct: 194 LFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTIIAAMVG 253 Query: 249 ERGGLAVADAAARGALPADTAVALELKELTGA---------DYEGVSFTVKRGEVVGLTG 299 + DA R L +++L+ A +GVSF V+ GE++G+ G Sbjct: 254 RN----LLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGG 309 Query: 300 ATSSGRTSVAEAI-AGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLT 358 +GRT + E I A + G I +DG + + G V +DR +GL L Sbjct: 310 LLGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLH 369 Query: 359 QSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVV 418 +S+ +N ++ + L +FG+ + + A + +DALG+ G LSGGNQQKVV Sbjct: 370 ESIRDNVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVV 429 Query: 419 MARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRV 477 + + LAT P VL+L +PT G+DV +K + ++ ++ +G A++VVS EL + L DR+ Sbjct: 430 IGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRI 489 Query: 478 LVMFRGR 484 LVM GR Sbjct: 490 LVMAEGR 496 Lambda K H 0.318 0.134 0.377 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: 651 Number of extensions: 43 Number of successful extensions: 7 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: 510 Length of database: 526 Length adjustment: 35 Effective length of query: 475 Effective length of database: 491 Effective search space: 233225 Effective search space used: 233225 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: 52 (24.6 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