Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 576 bits (1484), Expect = e-169 Identities = 292/493 (59%), Positives = 376/493 (76%), Gaps = 1/493 (0%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L GL+K F +KAL +VDF+L GEI ALLGENGAGKSTLIK +TGV+ D GT+ L Sbjct: 14 LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 G I+P++ A + GI TVYQEVNLLPN+SVA NL++GR+P RFG++R+ EM +RA Sbjct: 74 AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHA 133 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L+ YG +DV PL +SVA+Q I AI RA+DLSA+VLILDEPTASLD EVE+LF +M Sbjct: 134 LLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVM 193 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248 R+L G+ ++FV+HFLDQVY++ DR+TVLRNG +G R+ +LP+++L++MMLGREL Sbjct: 194 RKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLDLIRMMLGRELAE 253 Query: 249 HALQRAGRTLLSDKPVA-AFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 +RA + + V +FK +GK+G +APFDLE+R GE+VGLAGLLGSGRTETA ++F Sbjct: 254 TTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARLVF 313 Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367 G + ADSG A + GK L SP A+ LG G+CPE+RKT+GI+A +VRENI+LALQA+R Sbjct: 314 GAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQARR 373 Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427 G RP+SR+EQ EIA R+IR L IR P E+PI LSGGNQQK LL+RWL T P+ L+LD Sbjct: 374 GLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLLVLD 433 Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487 EPTRGIDVGAHAEIIRL+ LC GLALLVISSEL+E+V Y++RV+++RDR V E+ Sbjct: 434 EPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEELKGD 493 Query: 488 ELSVPAIMNAIAA 500 + V +I+ AIAA Sbjct: 494 AVEVSSILAAIAA 506 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: 678 Number of extensions: 29 Number of successful extensions: 6 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: 516 Length adjustment: 34 Effective length of query: 466 Effective length of database: 482 Effective search space: 224612 Effective search space used: 224612 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