Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 278 bits (712), Expect = 2e-79 Identities = 166/479 (34%), Positives = 264/479 (55%), Gaps = 6/479 (1%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 ++ + + K FPG+ A DNV +++GEI ALLGENGAGKSTL+ L G+Y ++G I + Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 +G+ + + A +LGIG V+Q L+ +V +N+ +G+EP G + K+ K Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVET 123 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 + YG ++D + SV MQQ V I + + A++LI DEPTA+L QE+ L +M Sbjct: 124 ISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIM 183 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248 ++L G S+I +TH L ++ +V DR TV+R G +G + E L MM+GRE++ Sbjct: 184 KKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVNF 243 Query: 249 HALQRAGR---TLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305 + + +L K + K+ + LEV GEI+G+AG+ G+G+TE E Sbjct: 244 SVEKDPAQPKDAVLQIKDLVV-KDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEA 302 Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365 I G++ G + G+ +P + + G+G P+DR G++ +V ENI+L Sbjct: 303 ITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYY 362 Query: 366 QRGWLRP--ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423 Q+ + ++ E + A I +RTPS LSGGNQQK +++R + P Sbjct: 363 QKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDL 422 Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVA 482 LI +PTRG+DVGA I + G A+L+IS EL+E++ +DR+ ++ + K VA Sbjct: 423 LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVA 481 Score = 95.9 bits (237), Expect = 3e-24 Identities = 60/208 (28%), Positives = 113/208 (54%), Gaps = 6/208 (2%) Query: 281 LEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFC 340 L+V+ GEI L G G+G++ V+FG+ + G L+KGKP + P+ A+ LGIG Sbjct: 25 LQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVKGKPVKITDPNVANRLGIGMV 84 Query: 341 PEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPI 400 + ++ +V ENIIL + G I+ K+ + E +Q G+ + I Sbjct: 85 HQHFM---LVEKFTVTENIILGKEPTAGG--KINIKKAAKAVETISKQYGLAVDPYAK-I 138 Query: 401 EFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISS 460 + +S G QQ+V + + L + LI DEPT + E+I++++ L ++G ++++I+ Sbjct: 139 QDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLVSEGKSIILITH 198 Query: 461 ELEELVGYADRVIIMRDRKQVAEIPLAE 488 +L+E++ DR ++R + + + ++E Sbjct: 199 KLKEIMEVCDRCTVIRRGRGIGTVDISE 226 Score = 94.4 bits (233), Expect = 9e-24 Identities = 68/234 (29%), Positives = 117/234 (50%), Gaps = 16/234 (6%) Query: 22 VKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHA 81 + A++++ + GEI+ + G +G G++ LI+A+TG+ G I L GQ I+ Sbjct: 270 ITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDITGLTPRKI 329 Query: 82 QQLGIGTVYQEVN---LLPNMSVADNL----FIGREPKRFGLLRRKEMEKRATELMASYG 134 G+G + Q+ + L+ + +V +N+ + + G+L E+ K+A EL+ Y Sbjct: 330 TGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKANELIEDY- 388 Query: 135 FSLDVREPLNR-----FSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189 DVR P S QQ I R +D S +LI +PT LD +E + + Sbjct: 389 ---DVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIHHRLV 445 Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243 + RD+G +++ ++ LD+V VSDRI V+ G V + + + EL +M G Sbjct: 446 KERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAG 499 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: 585 Number of extensions: 26 Number of successful extensions: 7 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: 509 Length adjustment: 34 Effective length of query: 466 Effective length of database: 475 Effective search space: 221350 Effective search space used: 221350 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