Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 245 bits (625), Expect = 1e-69 Identities = 145/327 (44%), Positives = 195/327 (59%), Gaps = 11/327 (3%) Query: 24 LRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKN-VVGMPPRDRDI 82 L+ +D+ + GE ++L+GPSGCGK+T L IIAGL+ P G + + G N V +P R + Sbjct: 23 LQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGDNDVTPLPIEQRGV 82 Query: 83 AMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGG 142 MVFQSYAL+P ++VA+NI + L +R++ R++R+DE+ AM+ + +RR QLSGG Sbjct: 83 GMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRIDQLSGG 142 Query: 143 QRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEA 202 QRQRVA+ RA+A QP++ L DEPL+ LDAKLR +RA+I +L ++ IT+VYVTHDQ EA Sbjct: 143 QRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSLHITAVYVTHDQAEA 202 Query: 203 MTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGA-------VTGGQ 255 M LG RI VM G + Q GTP +IY PAN +VA FIG TMN L V GG Sbjct: 203 MALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIG--TMNRLPAVLEADAWRVPGGL 260 Query: 256 FGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVEPTGPDTYVMVDTAA- 314 G A +LA PS E+L L E A G V G T ++VD A Sbjct: 261 VPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTALFLGNYTRLLVDVGAP 320 Query: 315 GSVTLRTDAQTRVQPGEHVGLALAPAH 341 + + T + G+ VGL L H Sbjct: 321 APLVVDTTRRDGWLAGDRVGLRLDTGH 347 Lambda K H 0.318 0.135 0.388 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: 329 Number of extensions: 8 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: 355 Length of database: 357 Length adjustment: 29 Effective length of query: 326 Effective length of database: 328 Effective search space: 106928 Effective search space used: 106928 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: 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