Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_009140593.1 HMPREF9452_RS02825 ATP-binding cassette domain-containing protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000225705.1:WP_009140593.1 Length = 356 Score = 155 bits (392), Expect = 2e-42 Identities = 116/364 (31%), Positives = 177/364 (48%), Gaps = 31/364 (8%) Query: 8 NVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILV--- 64 ++ K Y PD ++ L+ GE + L+G SGCGKS + CIAG+ET G I V Sbjct: 6 DIKKAY----PDFSLDVRLEAA-GERVALLGASGCGKSCTLRCIAGVETPDEGRIAVNGV 60 Query: 65 ---DDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121 D A +SP+ R A++FQ+Y L+P +SV DN+ G++ R DE R Sbjct: 61 TFFDSARGINLSPQQRKCALLFQNYQLFPNLSVADNVLAGVEGRLSREGR-DELARRYLS 119 Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 + + R P +LSGGQQQRVA+ R LA RP IY+FDEP S LD+ L+ + + + Sbjct: 120 IFGMAGYADRYPARLSGGQQQRVALARMLAARPAIYMFDEPFSALDSFLKSALEQNLLDL 179 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241 + +T +YV+HD EA L +++ V+ +G +++ GT + + P L G Sbjct: 180 FSVIDSTVLYVSHDIDEACRLCERICVLHNGRVEEDGTVEQVVQRPQTLAALRLTGCKNT 239 Query: 242 NFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGL 301 + R ++ L+ LD G +G A + D LG+R + N EA G Sbjct: 240 S----RARKVGDTLVEALDWGMT---FDVG---APVADDVAYLGVRANYFHIDNREAPGK 289 Query: 302 PTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRL-------APDVA--PAVGETLTLQFDPA 352 + V + + LV ++ RL D+A P G+ L + FD A Sbjct: 290 NSYMLRVARVSDSRFERLVLLDPPRADASSRLTWKVNTVGADMATLPREGDCLRMHFDAA 349 Query: 353 KVLL 356 K+L+ Sbjct: 350 KILM 353 Lambda K H 0.319 0.138 0.393 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: 343 Number of extensions: 15 Number of successful extensions: 4 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: 386 Length of database: 356 Length adjustment: 30 Effective length of query: 356 Effective length of database: 326 Effective search space: 116056 Effective search space used: 116056 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 (21.7 bits) S2: 49 (23.5 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