Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__BFirm:BPHYT_RS01820 Length = 544 Score = 424 bits (1091), Expect = e-123 Identities = 225/495 (45%), Positives = 323/495 (65%), Gaps = 4/495 (0%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L + + F GV AL + + S+ GE+ AL+G+NGAGKST+IK LTG Y G++ Sbjct: 18 LLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGSVRF 77 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 EG+ + + A++ GI T+YQE+NL+P SVA+N+F+GREP+RFGL+ +++RA Sbjct: 78 EGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWHAVQQRAAA 137 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L+ S+G +DV++P+ R+S A+QQ+VA+ RA+ AK++I+DE T+SLD +EVELLF ++ Sbjct: 138 LLESFGLQIDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELLFTVV 197 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL-- 246 R+LRD G ++IFV+H LD++Y + DR+TV+R+G V ++ +++LV MLGR L Sbjct: 198 RKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMADMDKLQLVTTMLGRTLAA 257 Query: 247 --DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304 A R K + A ++ LEV GE VGLAGLLGSGRTET Sbjct: 258 VVQDDAEAREANLARRGKQMIAATQLSAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETMR 317 Query: 305 VIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ 364 ++FG P + G+ I G+ L+SP A G+ + EDRK +GI+ SVR+N+ L Sbjct: 318 LMFGADPLERGSLSIGGETVALKSPQDAISRGLAYLTEDRKAEGIVPELSVRDNLTLVCL 377 Query: 365 AQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424 + K+QQ I +RFI LGI+ S +QPI LSGGNQQKVLL+RWL P L Sbjct: 378 RTLAKNGVVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAEPSLL 437 Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEI 484 +LDEPTRGIDVGA AE+ +++ L GLA+L+ +SELEEL ADR +++RD + VAE+ Sbjct: 438 LLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSASELEELTAVADRAVVIRDGRTVAEL 497 Query: 485 PLAELSVPAIMNAIA 499 A++S AIM+AIA Sbjct: 498 NGADMSETAIMDAIA 512 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: 650 Number of extensions: 26 Number of successful extensions: 7 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: 544 Length adjustment: 35 Effective length of query: 465 Effective length of database: 509 Effective search space: 236685 Effective search space used: 236685 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