Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_017548756.1 C792_RS0107025 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_000330705.1:WP_017548756.1 Length = 319 Score = 176 bits (445), Expect = 8e-49 Identities = 95/236 (40%), Positives = 147/236 (62%), Gaps = 8/236 (3%) Query: 32 DILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNI 91 ++ R G ++D++ I G+ FV++G SG GK+T ++ INRLI T+G + F I Sbjct: 6 NVTKRYGNKTAVDDLTFDIKEGETFVLIGPSGCGKTTTLKMINRLIPLTNGYIYFKDRPI 65 Query: 92 LDLGAKALRAFRMR-RVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDT 150 D + + MR + V Q AL PH T+ +N+ ++ S+ D + + ++ Sbjct: 66 SDY-----QVYEMRWDIGYVLQQIALFPHMTIKENIAQVPLMKKWSETDIDKRIDELLEM 120 Query: 151 VGLSG--YDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQ 208 VG+ + + P +LSGG +QRVG+ RALAAD VILMDE FSALDP+ R +QD L++ Sbjct: 121 VGMDPEQFKNRKPSELSGGQQQRVGVVRALAADPPVILMDEPFSALDPISREKLQDDLVE 180 Query: 209 LQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 LQ+ + KTIVF+THD+ EAL++G I +L++G Q+GTP++ L +P ND+V F+ Sbjct: 181 LQKKIKKTIVFVTHDIQEALKLGDRICLLKEGHAEQIGTPDEFLTSPRNDFVKDFI 236 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: 225 Number of extensions: 13 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: 319 Length adjustment: 26 Effective length of query: 249 Effective length of database: 293 Effective search space: 72957 Effective search space used: 72957 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 24 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