Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_089136416.1 CES79_RS04320 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_002217945.1:WP_089136416.1 Length = 314 Score = 168 bits (426), Expect = 2e-46 Identities = 101/258 (39%), Positives = 147/258 (56%), Gaps = 9/258 (3%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 +++ +NK + + L + + + GE +LVGPSG GK+TLL I L PT G+ Sbjct: 2 IELLNVNKEY----QEQHALDHLSLTINDGELFVLVGPSGSGKTTLLKTINRLVVPTSGQ 57 Query: 65 IRIGGKNV--VGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 ++I GK+V V + R I V Q+ AL+P ++VA+N L+ K P ++ +RI E+ Sbjct: 58 VKIDGKDVADVDLQQLRRRIGYVLQTGALFPNMTVAENASVQLDNLKWPAEKKHERIAEL 117 Query: 123 AAMLQIS--HLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 + + H LDR PS+LSGG+ QRV + RALA +P L L DE S LD R +++ Sbjct: 118 MTEVGLDPDHFLDRMPSELSGGEAQRVGIVRALAAKPGLVLMDESFSALDPVSRRQLQQI 177 Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 + LH+ T V+VTHD EA+ L RIAV+ G +QQ+GTP EI PAN +V++F Sbjct: 178 VINLHRDLDSTIVFVTHDMHEALRLADRIAVVYNGKLQQVGTPTEILTEPANAFVSSFFA 237 Query: 241 SPTM-NLLRGAVTGGQFG 257 + L G V FG Sbjct: 238 DEQQTDQLLGQVLAAGFG 255 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: 259 Number of extensions: 10 Number of successful extensions: 4 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: 314 Length adjustment: 28 Effective length of query: 327 Effective length of database: 286 Effective search space: 93522 Effective search space used: 93522 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 24 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