Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 171 bits (432), Expect = 3e-47 Identities = 90/222 (40%), Positives = 136/222 (61%), Gaps = 6/222 (2%) Query: 43 LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102 ++DVSL I G+IF ++G SGSGKSTL+R + PT G + DG +I DL Sbjct: 36 VDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDITDLPPYE---- 91 Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPH 162 R ++M+FQS+AL PH TV QN+ +G + +SK D + + + V + Y + PH Sbjct: 92 --RPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAKRKPH 149 Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITH 222 QLSGG +QRV LAR+LA ++L+DE ALD +R MQ +++++ + T V +TH Sbjct: 150 QLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTH 209 Query: 223 DLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 D +EA+ + IAI+ DG + QVG+P DI ++P + +A F+ Sbjct: 210 DQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFI 251 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: 265 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: 378 Length adjustment: 28 Effective length of query: 247 Effective length of database: 350 Effective search space: 86450 Effective search space used: 86450 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