Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 397 bits (1021), Expect = e-115 Identities = 240/530 (45%), Positives = 325/530 (61%), Gaps = 23/530 (4%) Query: 3 DMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGA 62 D T + P+LA I K+F GV AL+ V AGE+HALMGENGAGKSTLMK+LSG Sbjct: 8 DSVTTESDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGV 67 Query: 63 YTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL- 121 YT D G +DG+ V+ + A G+A+I+QEL+L P L VA+NI+LGR GL Sbjct: 68 YT-DYEGAVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLF 126 Query: 122 VARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPL 181 V R + A L RLG + P A V L + ++QLVEIA+A+ EARIL+MDEPT+ L Sbjct: 127 VDRKASLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSAL 186 Query: 182 STHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAA 241 S E RLF ++RQL +G+ I+YISHR+ E+ +L+DRVTV RDG V A L + Sbjct: 187 SPGECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENT 246 Query: 242 LVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVA---DGRR-----VKGCSFDLRAGEVL 293 ++ MVGR+L + + G+ E +LSVRD++ GR +KG SFD+RAGE+L Sbjct: 247 IIAAMVGRNLLDAHRRDRGKG-GGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEIL 305 Query: 294 GLAGLVGAGRTELARLVFGADARTR-GEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLT 352 G+ GL+GAGRTE+ +F ++ R GE+R+ + + PR A G A +T Sbjct: 306 GIGGLLGAGRTEILETIFASNEGLRGGEIRLDG-------IAVNIRSPRDARRLGFALVT 358 Query: 353 EDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNV 412 EDRK +GL L +S+ +N+ L + R A G + R A+D LG+R A Sbjct: 359 EDRKAKGLHLHESIRDNVALPLVGRLA-RFGLRSFEGERALAKGAVDALGVRCAGTGQAA 417 Query: 413 GALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISS 472 G LSGGNQQKV++ + L PRVL+LDEPTRG+D+GAK EIY LI LA G+AI+++SS Sbjct: 418 GTLSGGNQQKVVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSS 477 Query: 473 ELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAPA 522 ELPE++ L DR+LVM EG G + ++ERI+ LA +A A Sbjct: 478 ELPELLLLADRILVMAEGRQTGLI---SREEASEERIMQLAAPRSARGRA 524 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: 713 Number of extensions: 42 Number of successful extensions: 10 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: 526 Length adjustment: 35 Effective length of query: 505 Effective length of database: 491 Effective search space: 247955 Effective search space used: 247955 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 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