Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 283 bits (723), Expect = 7e-81 Identities = 159/345 (46%), Positives = 212/345 (61%), Gaps = 14/345 (4%) Query: 19 VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78 VL +D+H+ GEF++L+GPSGCGKST+L +IAGL++ + G +RIGG V +P R+R++ Sbjct: 23 VLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDI 82 Query: 79 AMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGG 138 AMVFQ+YALYP +SV DNI F L K P E +R+ EVAA+L + LL+R+P +SGG Sbjct: 83 AMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGG 142 Query: 139 QQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEA 198 Q+QR A+ RA+ + P +FLFDEPLSNLDAKLR ++R +IKRLHQ T+VYVTHDQ+EA Sbjct: 143 QRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEA 202 Query: 199 MTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIET 258 MTL R+ +M+ G + Q G+P E+Y P N + A FIG+P MN L G V GQ I+ Sbjct: 203 MTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAV--TGGQFGIQG 260 Query: 259 AHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGADALL 318 A A A V L VRP+H+ + E P V +VE G D + Sbjct: 261 AALNLAPPPS------SANEVLLGVRPEHL-VMQETAPWRG-----RVSVVEPTGPDTYV 308 Query: 319 TTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENL 363 ++T A QPG + LAL H FD +S E L Sbjct: 309 MVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERL 353 Lambda K H 0.321 0.137 0.403 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: 380 Number of extensions: 16 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: 406 Length of database: 355 Length adjustment: 30 Effective length of query: 376 Effective length of database: 325 Effective search space: 122200 Effective search space used: 122200 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: 50 (23.9 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