Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 167 bits (422), Expect = 4e-46 Identities = 93/226 (41%), Positives = 134/226 (59%), Gaps = 10/226 (4%) Query: 43 LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102 LN V L+I G++ ++G SGSGK+TL+R I L P +G+VLFDG ++ A A Sbjct: 18 LNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAAA---- 73 Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVR-GVSKDDAREIGMK---WIDTVGLSGYDA 158 RRV VFQ +AL H TV +N+ +G VR G K EI + + V L G Sbjct: 74 --RRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVELEGLGG 131 Query: 159 KFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIV 218 ++P QLSGG +QRV L+RALA V+L+DE F ALD +R ++ +L ++ T + Sbjct: 132 RYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDATGVTTI 191 Query: 219 FITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 F+THD +EAL + +AIL +G++ Q+GTP+ + D P +V FV Sbjct: 192 FVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFV 237 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: 231 Number of extensions: 14 Number of successful extensions: 3 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: 339 Length adjustment: 27 Effective length of query: 248 Effective length of database: 312 Effective search space: 77376 Effective search space used: 77376 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