Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 210 bits (535), Expect = 4e-59 Identities = 125/340 (36%), Positives = 191/340 (56%), Gaps = 20/340 (5%) Query: 6 VKNVSKVFKKG--KVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 + ++K F KG V L V+I++ GE ++GPSG GK+T + IIAGLD P+ GE+ Sbjct: 7 IAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIR 66 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123 + V +PP DR I MVFQ++ALYP L+ +NI F L KM K E +KR++E Sbjct: 67 IGGKNVVG-----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDE 121 Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183 VA +L I H+L+ P +LSGGQ+QRVA+ RAL + P L L DEP SNLDA++R RA + Sbjct: 122 VAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEI 181 Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243 K + G+T + V+HD + + R+ V+ G + Q+G P+++Y+ P + VA+ IG Sbjct: 182 KRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGS 241 Query: 244 --INELEGKVTNE--GVVIGSLRF-PVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGK 298 +N L G VT G+ +L P S++ ++G+RPE + + + W + Sbjct: 242 PTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETA----PW----R 293 Query: 299 GKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEV 338 G+V V+ G + + + T + + GE V Sbjct: 294 GRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHV 333 Lambda K H 0.319 0.139 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: 258 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: 353 Length of database: 355 Length adjustment: 29 Effective length of query: 324 Effective length of database: 326 Effective search space: 105624 Effective search space used: 105624 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