Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_1002 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1002 Length = 356 Score = 231 bits (588), Expect = 3e-65 Identities = 126/344 (36%), Positives = 205/344 (59%), Gaps = 14/344 (4%) Query: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 ++++I + KR+ G +V+ +++ +A G + L+GPSGCGKST L +IAG + T Sbjct: 11 AAIEIVALTKRYASGKPAVDA---INLRIASGSYCCLLGPSGCGKSTTLRMIAGHESVTS 67 Query: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 G+I + +N+ +P R AM+FQS+AL+P LS DN+ F+L+M+ +PK ERQ + ++ Sbjct: 68 GDILLENRNITDLPAAARGTAMMFQSFALFPHLSALDNVAFSLKMKGVPKAERQAKARDL 127 Query: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 + + HL +R+P++LSGGQ+QRVA+ RAL QP++ L DEPLS LD LR++MRAE++ Sbjct: 128 LERVALGHLAERKPAELSGGQQQRVALARALITQPRVLLLDEPLSALDPFLRIQMRAELR 187 Query: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 R + G+T ++VTH Q EAM L + VM GV++Q+G+P E+YNRPA+ +VA F+G Sbjct: 188 RWQKELGLTFIHVTHSQEEAMALADTMVVMNHGVIEQVGSPHEVYNRPASEFVARFMGGH 247 Query: 243 TMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVEPT 302 + G+ G++ L +AP ++ E+ G + L + ++G ++ Sbjct: 248 NVI----DTPEGKVGVRTDHLQIAP---ASAELPWGAQ-RMLAVVTDVEYQGTYVLLGLQ 299 Query: 303 GPDTYVMVDTAAGSVTLRTDAQTRVQP---GEHVGLALAPAHAH 343 + + A + ++A QP G+ V L P AH Sbjct: 300 KQGVALSANATAAYSVMVSEAAFAAQPYRVGQGVQLHWTPDQAH 343 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: 289 Number of extensions: 12 Number of successful extensions: 1 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: 356 Length adjustment: 29 Effective length of query: 326 Effective length of database: 327 Effective search space: 106602 Effective search space used: 106602 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