Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AO356_00615 AO356_00615 choline ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00615 Length = 407 Score = 241 bits (615), Expect = 2e-68 Identities = 127/268 (47%), Positives = 186/268 (69%), Gaps = 4/268 (1%) Query: 1 MADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMG 60 M+ I +V IF K AL +++ G + +IL ++G VG+ +L+I G+I V+MG Sbjct: 1 MSIIRFEDVDVIFAARPKPALELLDQGFSRPEILQKTGLIVGVEKANLEINKGEICVLMG 60 Query: 61 LSGSGKSTLVRHINRLIEPTSGEVLFDGD----NILDLGAKALRAFRMRRVSMVFQSFAL 116 LSGSGKS+L+R IN L + G++ + + +I L+ R +R++MVFQ FAL Sbjct: 61 LSGSGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCTPAELKMMRTQRIAMVFQKFAL 120 Query: 117 MPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLAR 176 MP TV +N+ +G ++G S+ + R++ + ++ VGL+ + K P +LSGGM+QRVGLAR Sbjct: 121 MPWLTVRENISFGLEMQGRSEKECRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLAR 180 Query: 177 ALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAI 236 ALA D D++LMDE FSALDPLIR +QD+LL LQR L KTIVF++HDLDEAL++G+ IAI Sbjct: 181 ALAMDADILLMDEPFSALDPLIRQGLQDELLDLQRKLHKTIVFVSHDLDEALKLGTRIAI 240 Query: 237 LRDGQVVQVGTPNDILDNPANDYVARFV 264 ++DG+++Q TP +I+ NPA+DYV FV Sbjct: 241 MKDGKIIQYSTPEEIVLNPADDYVRNFV 268 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: 311 Number of extensions: 13 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: 407 Length adjustment: 28 Effective length of query: 247 Effective length of database: 379 Effective search space: 93613 Effective search space used: 93613 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: 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