Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 365 bits (937), Expect = e-105 Identities = 191/492 (38%), Positives = 302/492 (61%), Gaps = 12/492 (2%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L +SK FPGV AL +V +R G ++AL+GENGAGKSTL+K + G+Y D G + L Sbjct: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR-FGLLRRKEMEKRAT 127 G+ ++ A Q GI ++QE+NL+P+MS+A+N++IGRE F ++ +EM + Sbjct: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 +L+ +LD E + S+A +Q+V I +A+ + +LI+DEPT+++ +EV LF + Sbjct: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 + L+ +G +I++TH +++V+ ++D + V R+G+++G + + L+ MM+GREL Sbjct: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 Query: 248 THALQRAGRTLLSDKPVA----AFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303 R +KP+ + ++ G ++ GEI+G+AGL+GSGRT A Sbjct: 267 QLFPVR-------EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVA 319 Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILAL 363 E IFGI P+D G + G+P + PH A G EDRK G+ SV EN+ +A+ Sbjct: 320 EAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 379 Query: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423 I +K + + E ++L ++TPS EQ I+ LSGGNQQK LL+RWL+T P+ Sbjct: 380 LPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 439 Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483 LILDEPTRGIDVGA AEI RLI L ++G+A+++ISSEL E++G +DRV++M + + Sbjct: 440 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 499 Query: 484 IPLAELSVPAIM 495 + +E + +M Sbjct: 500 LDRSEATQERVM 511 Score = 82.0 bits (201), Expect = 5e-20 Identities = 54/222 (24%), Positives = 109/222 (49%), Gaps = 6/222 (2%) Query: 28 VDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIG 87 V F L GEI+ + G G+G++ + +A+ G+ +D G I L+GQ + + A + G Sbjct: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354 Query: 88 TVYQE---VNLLPNMSVADNLFIGREPKRFG--LLRRKEMEKRATELMASYGFSL-DVRE 141 + ++ L P +SV +N+ + P G +++K + ++ + + Sbjct: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414 Query: 142 PLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFV 201 ++ S QQ + R + + ++LILDEPT +D ++ L+ L G+++I + Sbjct: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474 Query: 202 THFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243 + L +V +SDR+ V+ G +G + E Q ++++ G Sbjct: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516 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: 592 Number of extensions: 28 Number of successful extensions: 8 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: 521 Length adjustment: 34 Effective length of query: 466 Effective length of database: 487 Effective search space: 226942 Effective search space used: 226942 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