Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 166 bits (421), Expect = 5e-46 Identities = 93/245 (37%), Positives = 140/245 (57%), Gaps = 6/245 (2%) Query: 20 ALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEP 79 A+T + + ++ R G +++VSL + G+ F ++G SG GK+TL+R + P Sbjct: 7 AMTTPKPIITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETP 66 Query: 80 TSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDD 139 T G +L DG +I ++ R V+MVFQS+A+ PH TV NV YG +V V K + Sbjct: 67 TEGRILIDGQDISNVPPNK------RPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAE 120 Query: 140 AREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIR 199 + ++ V L G + P QLSGG +QRV LARAL V+L+DE SALD +R Sbjct: 121 REARVAEALELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLR 180 Query: 200 GDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDY 259 M+ +L LQ + T + +THD DEAL + S A++ G + QV TP+D+ + P + + Sbjct: 181 EQMRTELCTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRF 240 Query: 260 VARFV 264 VA F+ Sbjct: 241 VADFI 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: 227 Number of extensions: 9 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: 381 Length adjustment: 28 Effective length of query: 247 Effective length of database: 353 Effective search space: 87191 Effective search space used: 87191 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