Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 161 bits (408), Expect = 2e-44 Identities = 86/225 (38%), Positives = 139/225 (61%), Gaps = 6/225 (2%) Query: 40 TVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKAL 99 T+ +++V+L I G+IF ++G SGSGKSTL+R + P +G ++ DG ++ AL Sbjct: 27 TLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLDGQDVT-----AL 81 Query: 100 RAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAK 159 F +R +M+FQS+AL PH TV QN+ G + + K + R+ + V + Y + Sbjct: 82 PPF-LRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKMEPYARR 140 Query: 160 FPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVF 219 P QLSGG +QRV LAR+LA ++L+DE ALD +R +MQ +L+++ N+ T + Sbjct: 141 KPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENVGATCLM 200 Query: 220 ITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 +THD +EA+ + S IAI+ G++ Q+G+P DI ++P + A F+ Sbjct: 201 VTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFI 245 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: 245 Number of extensions: 11 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: 372 Length adjustment: 28 Effective length of query: 247 Effective length of database: 344 Effective search space: 84968 Effective search space used: 84968 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