Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate WP_011841069.1 RSPH17029_RS07670 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >NCBI__GCF_000015985.1:WP_011841069.1 Length = 369 Score = 330 bits (845), Expect = 5e-95 Identities = 182/356 (51%), Positives = 242/356 (67%), Gaps = 8/356 (2%) Query: 1 MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTI 60 MA LK+ ++K + +++ IDL + E +VFVGPSGCGKSTLLR+IAGLE +T GT+ Sbjct: 1 MADLKLTGVEKAYGEVRVLRDIDLTIEKGELIVFVGPSGCGKSTLLRMIAGLERITGGTL 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARI 120 E+DG+ + +V PA+R +AMVFQ+YALYPHM+VR+NM FAL +AG +KAE+ + V AARI Sbjct: 61 EIDGQVVNDVPPAQRGIAMVFQSYALYPHMTVRQNMEFALKIAGQSKAEIARAVENAARI 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L+L P L+R P+ LSGGQRQRVAIGRAIVR+PK++LFDEPLSNLDAALRV R+E+A+L Sbjct: 121 LQLTPYLDRLPRALSGGQRQRVAIGRAIVRDPKVYLFDEPLSNLDAALRVATRIEIAQLK 180 Query: 181 KEL-QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 +++ TMIYVTHDQVEAMTLA ++VVL GG I QVG+PLELY +P N FVA F+G+P M Sbjct: 181 EKMPDRTMIYVTHDQVEAMTLASRIVVLEGGGISQVGTPLELYTRPRNAFVARFIGSPAM 240 Query: 240 GFLKGKVTRVERQNCEVLLDAG--TRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCT 297 L G++ + V LD+G R +P +L G V LG+RPE L + G Sbjct: 241 NLLPGEIVETGPETV-VRLDSGGVARTAIPTEPEDL--GLLVDLGVRPEDL-VKTDGPPL 296 Query: 298 LQVTADVSERLGSDTFCH-VLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLF 352 + +++E LG T + V G + ++ G A + L D HLF Sbjct: 297 YEGEVEITEALGEVTLLYFVPRDEGGQVVAKLPGIQADLRHRTVRLGADPARLHLF 352 Lambda K H 0.321 0.137 0.390 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: 384 Number of extensions: 14 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: 367 Length of database: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. 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