Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 458 bits (1178), Expect = e-133 Identities = 246/480 (51%), Positives = 329/480 (68%), Gaps = 4/480 (0%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L+ GL K F ALD VD +LR GE+ AL+G+NGAGKSTLIK LTGV DRG++ L Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR--FGLLRRKEMEKRA 126 +G+ I+P AQ+ GIGTVYQEVNL PN+SVA+NL+ GR P+R ++ +++ A Sbjct: 72 DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131 Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186 L+ LDV PL + VA++Q+VAI RA+ +SA+VLILDEPT+SLD EV LF Sbjct: 132 RSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFR 191 Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL 246 ++ QLR+RG++++FVTHFLDQVY VSDRITVLR+G VG +LP LV M+GR+L Sbjct: 192 VIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRDL 251 Query: 247 DTHALQRAGRTLLSDKPVAA-FKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305 T A A R D P A + G +G + P DL+VR GE++GL GLLGSGRTE A + Sbjct: 252 PTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARL 311 Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365 +FG+ A+ G I G+ L+ P A V G+ CPE+RKTDGI+A SVRENI+LALQA Sbjct: 312 LFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLALQA 371 Query: 366 QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLI 425 ++GW R +SR Q E+A + ++ LGI+ E P+ LSGGNQQKV+L+RWL+T P+ LI Sbjct: 372 RQGW-RGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRLLI 430 Query: 426 LDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIP 485 LDEPTRGIDV A E++ + G+A+L IS+E EL + DR+ +MR+R++ E+P Sbjct: 431 LDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAGELP 490 Score = 95.9 bits (237), Expect = 3e-24 Identities = 65/231 (28%), Positives = 119/231 (51%), Gaps = 4/231 (1%) Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 K +G + DL +R GE+ L G G+G++ +++ G++ D G+ + G+ Sbjct: 20 KRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELDGRVIAPS 79 Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIR 387 +P +A GIG ++ + SV EN+ +R LR I ++ ++ A +R Sbjct: 80 TPMEAQRDGIGTVYQEVN---LCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGARSLLR 136 Query: 388 QLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIET 447 QL + + P+ +Q V ++R L + LILDEPT +D G E+ R+I Sbjct: 137 QLHLEL-DVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRVIAQ 195 Query: 448 LCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAI 498 L G+A+L ++ L+++ +DR+ ++RD +V E +A+L A++NA+ Sbjct: 196 LRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAM 246 Lambda K H 0.321 0.138 0.391 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: 684 Number of extensions: 30 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 505 Length adjustment: 34 Effective length of query: 466 Effective length of database: 471 Effective search space: 219486 Effective search space used: 219486 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 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