Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_084934993.1 HA51_RS13475 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_002095475.1:WP_084934993.1 Length = 500 Score = 374 bits (959), Expect = e-108 Identities = 218/514 (42%), Positives = 323/514 (62%), Gaps = 22/514 (4%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 LL LR I K F V+AL++V+LT AGE+HAL GENGAGKSTLM I+ G D GE Sbjct: 4 LLELRGISKRFGAVKALQEVDLTLQAGEIHALAGENGAGKSTLMNIIDGILRPD-SGEIW 62 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132 +DG+ V I P+ A+ LG+ +++QE++L P++S+ ENI++ A Q+RGL+ +R A Sbjct: 63 LDGKPVTIRSPREAQQLGIGLVHQEIALCPDISIYENIWM--AHQQRGLLLPHKALRERA 120 Query: 133 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 192 + A + V LS++Q+QLVEIA+A+ + R+L++DEPT L+ E LF++ Sbjct: 121 QQVMNRLAPIPVSKKVGELSLSQQQLVEIAKALTLDCRLLILDEPTAALTEPEAQTLFSI 180 Query: 193 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252 +RQLR +GM ++YISHRMAEI L +T+LRDG V + A ++ ++ +VGR+LS Sbjct: 181 VRQLRDQGMTVVYISHRMAEIFALCQHITILRDGRTVHSAPLASMTADEVITRLVGRELS 240 Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312 Y + +L VR+++DG+R F+LR GE+LG+ GL+GAGR+E+A+ + Sbjct: 241 QLYPDKR-PVNDAPPLLEVRNISDGKRFHDIHFNLRPGEILGIGGLMGAGRSEIAQGICA 299 Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372 TRG +RI G V L +I + YL+EDRK GLFL + NI+ Sbjct: 300 LQPLTRGSIRI-----KGEPVRLKDYAA--SIQQRMVYLSEDRKDAGLFLAMPIDWNIS- 351 Query: 373 IVAARDALGLGRLNRTAARRRTTEAIDTLG--IRVAHAQVN--VGALSGGNQQKVMLSRL 428 A D + T + RR + L +++ +++ V +LSGGNQQKV L+R+ Sbjct: 352 ---ALDIRAVSHHGLTLSPRRERLQAEALAQQVKLKRGKLSDPVSSLSGGNQQKVALARV 408 Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488 L +QP ++ LDEPTRGVD+ AK+EIY+++ LA +GV +++ISSELPE++GLCDR++V+ Sbjct: 409 LSVQPEIVFLDEPTRGVDVSAKAEIYQILANLAGNGVGLVVISSELPELIGLCDRIIVIH 468 Query: 489 EGTLAGEVRPAGSAAETQERIIALATGAAAAAPA 522 EG ++GEV AA T+E ++ LA G A A A Sbjct: 469 EGRISGEVT---GAAMTEENLMRLAAGIATQAEA 499 Lambda K H 0.320 0.136 0.382 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: 622 Number of extensions: 25 Number of successful extensions: 8 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: 540 Length of database: 500 Length adjustment: 35 Effective length of query: 505 Effective length of database: 465 Effective search space: 234825 Effective search space used: 234825 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 (21.8 bits) S2: 52 (24.6 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