Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 386 bits (991), Expect = e-111 Identities = 230/515 (44%), Positives = 315/515 (61%), Gaps = 15/515 (2%) Query: 6 DTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTA 65 D +L L+ + K FPGV AL ++L +GEVHA+ GENGAGKSTLMKI+SG Y A Sbjct: 15 DVPAPREILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHA 74 Query: 66 DPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARG 125 D G C+ +G+ VQ A+ G+A+I+QEL+L P+LSVAENIYL R +R V Sbjct: 75 DDGVICY-EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYR 133 Query: 126 DMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHE 185 + L R+G + SP V +LSIAQ+Q+VEIA+A+ +AR+L+MDEPT+ L+ E Sbjct: 134 TLNANAQRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESE 193 Query: 186 TDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKM 245 T +LF +IR+LR +G+AILYISHR+ E+ E+ DRVTVLRDG + T D A + +V Sbjct: 194 TVQLFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVAR 253 Query: 246 MVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTE 305 MVGR L Y E +V++ VRD+ SFDLR GE+LG AGL+GAGRTE Sbjct: 254 MVGRALDDAYPPRESVPTE-QVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTE 312 Query: 306 LARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQS 365 +AR +FGA+ G +++ G + PR+AI GIAYL+EDRK GL L Sbjct: 313 VARAIFGAERLDSGSIQL-------GDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMP 365 Query: 366 VHENINLI-VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVM 424 V NI L V A + G R + A + L IR + LSGGNQQK++ Sbjct: 366 VAANITLSNVRAISSRGFLRFSEETA--IAERYVRELAIRTPTVKQIARNLSGGNQQKIV 423 Query: 425 LSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRV 484 +S+ L R+L DEPTRG+D+GAK IY+L++ LA GV +++ISSELPE++G+ DR+ Sbjct: 424 ISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRI 483 Query: 485 LVMREGTLAGEVRPAGSAAETQERIIALATGAAAA 519 V EG + + + +QE I+ A+G + A Sbjct: 484 AVFHEGLITAVLE---TRQTSQEEILHYASGRSHA 515 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: 638 Number of extensions: 36 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: 515 Length adjustment: 35 Effective length of query: 505 Effective length of database: 480 Effective search space: 242400 Effective search space used: 242400 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