Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AZOBR_RS06950 AZOBR_RS06950 ABC transporter
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__azobra:AZOBR_RS06950 Length = 520 Score = 266 bits (681), Expect = 1e-75 Identities = 168/472 (35%), Positives = 253/472 (53%), Gaps = 10/472 (2%) Query: 10 LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69 L G++K FPG A D VD LR GEI ALLGENGAGKSTL+K + GV HAD G I Sbjct: 13 LELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN 72 Query: 70 GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129 G + A A++LGIG V+Q +L ++VA+N+ +G + G + + R E+ Sbjct: 73 GHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLGLDQP--GPI--DALSARIAEV 128 Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189 YG SLD R ++ SV +Q V I R + K+LI+DEPT+ L QE LF+ +R Sbjct: 129 SERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETLR 188 Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDTH 249 +L G ++++++H L+++ + D TVLR G VG + L +MM+G EL T Sbjct: 189 RLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEMMIGTELSTP 248 Query: 250 ---ALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306 AG L + ++ + + EVR GEI+G+AG+ G+G+ E + Sbjct: 249 ERLPQGEAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAAL 308 Query: 307 FG-IKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365 G D + I+G+P P + +LG+ F PE+R G + S+ EN +L+ A Sbjct: 309 SGEALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLSENALLSGYA 368 Query: 366 QRGWLRP--ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423 + +R + + AER I + T LSGGN QK ++ R +L +P+ Sbjct: 369 REPLVRSGLVHFGRARSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPRL 428 Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475 L++ +PT G+D GA A I R + L G A+LVIS +L+EL +DR+ ++ Sbjct: 429 LVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIAVL 480 Score = 85.1 bits (209), Expect = 5e-21 Identities = 64/202 (31%), Positives = 101/202 (50%), Gaps = 10/202 (4%) Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339 DL +RPGEI L G G+G++ ++I+G+ AD+G G ++ P A LGIG Sbjct: 32 DLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWNGHDTHIPDPAGARRLGIGM 91 Query: 340 CPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQP 399 + + +V ENI L L Q G + +S + E++ER+ L R + Sbjct: 92 VFQHFS---LFDTLTVAENISLGLD-QPGPIDALSARIA-EVSERYGLSLDPR-----RH 141 Query: 400 IEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVIS 459 + LS G +Q+V + R LL P+ LI+DEPT + + + L A+G +L IS Sbjct: 142 VHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETLRRLAAEGCTILYIS 201 Query: 460 SELEELVGYADRVIIMRDRKQV 481 +LEE+ D ++R + V Sbjct: 202 HKLEEIRALCDTATVLRGGRVV 223 Score = 63.9 bits (154), Expect = 1e-14 Identities = 57/233 (24%), Positives = 107/233 (45%), Gaps = 10/233 (4%) Query: 20 PGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTG-VYHADRGTIWLEGQAISPKNT 78 P L +V F +R GEI+ + G G G++ L+ AL+G D ++ +EG+ Sbjct: 273 PFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAALSGEALVPDPASVAIEGRPAGHLGP 332 Query: 79 AHAQQLGIGTVYQEV---NLLPNMSVADNLFIG---REPK-RFGLLRRKEMEKRATELMA 131 + LG+ V +E +P +S+++N + REP R GL+ A ++ Sbjct: 333 RERRLLGLAFVPEERLGRGAVPELSLSENALLSGYAREPLVRSGLVHFGRARSYAERIIG 392 Query: 132 SYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQ 190 ++ + R S Q I R I ++L++ +PT +D + + Sbjct: 393 AFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHRALID 452 Query: 191 LRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243 L G +++ ++ LD+++ +SDRI VL +G R T +E + +++G Sbjct: 453 LARAGAAVLVISQDLDELFVLSDRIAVLFHGHLSESRPT-HHTSVEEIGLLMG 504 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: 574 Number of extensions: 32 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 500 Length of database: 520 Length adjustment: 34 Effective length of query: 466 Effective length of database: 486 Effective search space: 226476 Effective search space used: 226476 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