Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Pf6N2E2_162 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_162 Length = 517 Score = 272 bits (696), Expect = 2e-77 Identities = 174/481 (36%), Positives = 265/481 (55%), Gaps = 17/481 (3%) Query: 30 LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89 L D+++ +M GE AL G NGAGKSTL I+ GL P TG+++F G + A Sbjct: 24 LTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEEL 83 Query: 90 RVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWKID-VREDARA 148 V V Q ++ LSVAENLF++ P GG I + +R+ A + +D + D Sbjct: 84 GVRMVMQELNLLPTLSVAENLFLDNLPNHGGWISRKQLRKAAIEAMAQVGLDAIDPDTLV 143 Query: 149 GDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTFLFISH 208 G+L + +Q+VEIAR L +ILDEPTA L E++ LF +I+ LQ GV+ ++ISH Sbjct: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVSIIYISH 203 Query: 209 HLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADAAARGALPADT 268 L+E+ + Q + VLRD + P++ EQL+ M G G + + PA Sbjct: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGEHIDLGPRQIGAPA-- 261 Query: 269 AVALELKELTGAD-YEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDG 327 L +K LT +D VSF V+ GE+ G++G +GRT + I G A GT+++ Sbjct: 262 ---LTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADTADSGTVALGS 318 Query: 328 -----AILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGIAAPA 382 +I P D ++AHGI + +DR EGL+LTQS+A N ++ + G+ Sbjct: 319 PAQVVSIRSPAD---AVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAGLVNGD 375 Query: 383 KKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVK 442 + A Q+ +DA+ I + P +VS LSGGNQQKVV+ R L + V++ +PT G+DV Sbjct: 376 AELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVG 435 Query: 443 SKEALLSVVDRVREEGKAVLVVSGELDDLR-TCDRVLVMFRGRVAAEFPA-GWQDHDLIA 500 +K + +++ + +GKA++VVS +L +L CDR+ V+ GR+ F W DL+A Sbjct: 436 AKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLA 495 Query: 501 S 501 + Sbjct: 496 A 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: 596 Number of extensions: 36 Number of successful extensions: 9 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: 517 Length adjustment: 35 Effective length of query: 475 Effective length of database: 482 Effective search space: 228950 Effective search space used: 228950 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