Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AZOBR_RS22795 AZOBR_RS22795 spermidine/putrescine ABC transporter ATPase
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__azobra:AZOBR_RS22795 Length = 358 Score = 170 bits (431), Expect = 4e-47 Identities = 97/232 (41%), Positives = 137/232 (59%), Gaps = 6/232 (2%) Query: 33 ILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNIL 92 I R G + +++V+L+I AG++ ++G SG GK+TL+R + T G V+ GD ++ Sbjct: 6 ITHRFGASTAVDNVTLEIKAGELVALLGPSGCGKTTLLRILAGFQAQTLGRVVI-GDRVV 64 Query: 93 DLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVG 152 D A R V +VFQ++AL PH TV QNV YG RG ++D R + V Sbjct: 65 DSLPPAGRG-----VGIVFQNYALFPHMTVAQNVAYGLEARGAARDAVRARVEAMLGLVK 119 Query: 153 LSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRN 212 L +FP QLSGG +QRV LARALA ++L+DE F+ALD +R DMQ ++ QLQR Sbjct: 120 LDAMRDRFPKQLSGGQQQRVALARALAIQPSILLLDEPFAALDKNLRLDMQIEIKQLQRR 179 Query: 213 LAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 T + +THD +EAL + IA+L G++ Q GTP D+ D P +V FV Sbjct: 180 FGITTIMVTHDQEEALSMADRIAVLSRGKLEQFGTPEDVYDRPGTLFVNGFV 231 Lambda K H 0.323 0.139 0.397 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: 212 Number of extensions: 12 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: 275 Length of database: 358 Length adjustment: 27 Effective length of query: 248 Effective length of database: 331 Effective search space: 82088 Effective search space used: 82088 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 (21.9 bits) S2: 48 (23.1 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