Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 293 bits (749), Expect = 1e-83 Identities = 188/508 (37%), Positives = 273/508 (53%), Gaps = 7/508 (1%) Query: 9 TSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDT 68 T+S P++ ++K F AL+ V V GE HAL+G NGAGKSTL+ LTG+ + D Sbjct: 7 TASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDA 66 Query: 69 GEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMR 128 G V G A +A R + VYQ ++ +LSVAENLF+ RQP+R G++D AMR Sbjct: 67 GTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMR 126 Query: 129 RDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188 R ARA+L + + + A G SV +Q+V IARA+ A+ +ILDEPTA LD E+ Sbjct: 127 RRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAV 186 Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248 LF+ + L+ G+ +F++H L +VY +C +TVLR+ R + + LPR L+ M G Sbjct: 187 LFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLG 246 Query: 249 ERGGLAVADAAARGALPADTAVALELKELTG----ADYEGVSFTVKRGEVVGLTGATSSG 304 R AVA A A A+ L G E ++ GEVVGL G SG Sbjct: 247 -RELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSG 305 Query: 305 RTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAEN 364 RT A + G+ A RG +VDG + ++ G G P+DR EG+V SV EN Sbjct: 306 RTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVREN 365 Query: 365 ASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALA 424 + + G ++ + I L I E + LSGGNQQK ++AR LA Sbjct: 366 IILALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLA 425 Query: 425 TNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDLRTCDRVLVMFRG- 483 T P +L+L +PT G+DV + ++ +++R+ +G A+LVVS EL+++ R +V+ R Sbjct: 426 TEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDR 485 Query: 484 RVAAEFPAGWQDHD-LIASVEGVSLHEE 510 R AE G D ++A++ S+ EE Sbjct: 486 RHVAELRGGEVAVDRIVAAIASESVPEE 513 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: 611 Number of extensions: 33 Number of successful extensions: 8 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: 516 Length adjustment: 35 Effective length of query: 475 Effective length of database: 481 Effective search space: 228475 Effective search space used: 228475 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