Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 301 bits (772), Expect = 3e-86 Identities = 177/515 (34%), Positives = 293/515 (56%), Gaps = 18/515 (3%) Query: 7 SSAPLSQP-FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65 S+ P ++P LE+ G+ K F + AL+ V + G+I+ LLGENG GKSTLIK+++G Sbjct: 5 SAPPAARPSLLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVF 64 Query: 66 PPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA 125 D G + + G A SA +A+ AGI TVYQ+++LLPN+SVA+N+ L + Sbjct: 65 ARDAGTVRLAGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQ 124 Query: 126 RTFDRRVLAATAARALEA-VGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMD 184 RR A L+ VG P + +A + + AIARA+ A+ +I+D Sbjct: 125 AEMRRRAHALLLDYGLDIDVGAP---------LASYSVAVQHITAIARAVDLSARVLILD 175 Query: 185 EPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA 244 EPT SL + EV+ L V+ L A G+ ++FVSH LD+ Y I V VLR+G+ + I Sbjct: 176 EPTASLDRHEVEILFRVMRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDIT 235 Query: 245 EFTKAQISELMTGRHLSNERYRESAH----AQDIVLDVRGFTRAGQFSDVSFKLHGGEIL 300 + + + +M GR L+ + +A A+++ + +GF + G + +L GE++ Sbjct: 236 DLPRLDLIRMMLGRELAETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVV 295 Query: 301 GVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGL 360 G+ GLL SGR E AR + G A SG+ + G+ + L +P DA GY PE+R EG+ Sbjct: 296 GLAGLLGSGRTETARLVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGI 355 Query: 361 FLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQ 420 D +R+N++ A + + R + R +A + ++ L I P ++P+ LSGGNQ Sbjct: 356 VADLTVRENIVLA-LQARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQ 414 Query: 421 QRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQN 480 Q+ L+ RWLA P++L+L PT G+DVG+ I R+++ L ++G+ +++IS +L E++ Sbjct: 415 QKALLARWLATSPKLLVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTY 474 Query: 481 CDRILMMK-KGHVSAEYRADELSEADLYHALLSEA 514 +R+++++ + HV E + D + + + A+ ++A Sbjct: 475 SNRVVVLRDRAHVE-ELKGDAVEVSSILAAIAADA 508 Lambda K H 0.319 0.135 0.376 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: 585 Number of extensions: 23 Number of successful extensions: 7 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: 515 Length of database: 516 Length adjustment: 35 Effective length of query: 480 Effective length of database: 481 Effective search space: 230880 Effective search space used: 230880 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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