Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 347 bits (891), Expect = e-100 Identities = 190/498 (38%), Positives = 301/498 (60%), Gaps = 16/498 (3%) Query: 7 QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66 + +L+ +G+ K FPGVKAL ++ G +MAL+GENGAGKST++K LTG+Y D GT+ Sbjct: 2 EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61 Query: 67 WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGRE-PKRFGLLRRKEMEKR 125 G+ + +Q+ GIG ++QE+NL+P +++A+N+F+GRE RFG + K M Sbjct: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121 Query: 126 ATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLF 185 A +L+A + + S+ QQ+V I + + +KV+I+DEPT +L E E LF Sbjct: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181 Query: 186 DLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE 245 ++R+L+ +G +++++H + +++++ D +TV R+G F+ RE L + L++MM+GR+ Sbjct: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241 Query: 246 LDT---HALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTET 302 L+ H + G L N G + +R GEI+G++GL+G+GRTE Sbjct: 242 LEDQYPHLDKAPGDIRLK------VDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTEL 294 Query: 303 AEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA 362 +V++G P SG + G RSP GI + EDRK DG++ SV+EN ++ Sbjct: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKEN--MS 352 Query: 363 LQAQRGWLRP---ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLT 419 L A R + R + ++Q+ FIR ++TPS EQ I LSGGNQQKV ++R L+T Sbjct: 353 LTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMT 412 Query: 420 RPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRK 479 RP+ LILDEPTRG+DVGA EI +LI ADGL+++++SSE+ E++G +DR+I+M + Sbjct: 413 RPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGH 472 Query: 480 QVAEIPLAELSVPAIMNA 497 E + + +M A Sbjct: 473 LSGEFTREQATQEVLMAA 490 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: 588 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: 500 Length of database: 501 Length adjustment: 34 Effective length of query: 466 Effective length of database: 467 Effective search space: 217622 Effective search space used: 217622 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