Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 344 bits (883), Expect = 2e-99 Identities = 188/373 (50%), Positives = 242/373 (64%), Gaps = 31/373 (8%) Query: 2 ATLELRNVNKTYGPG--LPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISG 59 ++L++ +NK +G G + L+ +++ + GEFLILVGPSGCGKSTL+N IAGL+ + Sbjct: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 Query: 60 GAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARV 119 G I + ++ GM P+DRDIAMVFQSYALYPT+SV DNI F L++RKMP E + + V Sbjct: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 Query: 120 SKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179 + +LQI HLL R+P QLSGGQ+QRVAMGRALAR+P+++LFDEPLSNLDAKLRVEMR E+K Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 Query: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSP 239 +HQ T+VYVTHDQ+EAMTLG ++AVMK G++QQ GTP +IYN PAN +VA+FIGSP Sbjct: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 Query: 240 PMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGL-------EDREVILGIRPEQII 292 MN L + GQ G+Q A L EV+LG+RPE ++ Sbjct: 243 TMNL-----------LRGAVTGGQ------FGIQGAALNLAPPPSSANEVLLGVRPEHLV 285 Query: 293 LANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPA 352 + R V V EPTGPDT V V+ V R GE + L PA Sbjct: 286 MQE-----TAPWRGRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPA 340 Query: 353 KVLLFDAKTGERL 365 FDA++ ERL Sbjct: 341 HAHWFDAQSEERL 353 Lambda K H 0.319 0.138 0.393 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: 437 Number of extensions: 17 Number of successful extensions: 3 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: 386 Length of database: 355 Length adjustment: 30 Effective length of query: 356 Effective length of database: 325 Effective search space: 115700 Effective search space used: 115700 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 (21.7 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