Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 227 bits (579), Expect = 7e-64 Identities = 152/478 (31%), Positives = 247/478 (51%), Gaps = 29/478 (6%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 ++R EG+ K F V+A ++ + G I ALLGENGAGKSTL+ L+G D G I + Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 +G+A+ ++ A + GIG VYQ L+ +M+VA+N+ +G+ L M + E Sbjct: 94 DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSG---AWLSPVHMSRVVAE 150 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L A YG +D + S+ +Q V I + + ++VLILDEPTA L E E LF+ + Sbjct: 151 LAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEAL 210 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELP-QIELVKMMLGR--- 244 ++ + G +++F++H + +V ++D I +LR G V E+P + EL M+GR Sbjct: 211 HRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVI 270 Query: 245 -ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303 E+ L+ R L D G KG EVR GE+ +AG+ G+G+ E Sbjct: 271 LEVAAEPLEPGDRVLHVD----GLAGDGLKG----LSFEVRKGEVFAIAGVAGNGQRELV 322 Query: 304 EVIFGIKPADSGTALIKGKPQN---LRSPHQASVLGIGFCPEDRKTDGIIAAASVRENII 360 E + G++ G + G P ++P Q G+ + PEDR+ + + +N + Sbjct: 323 ECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLATCLSLDLVDNFL 379 Query: 361 LALQA--QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLL 418 L + RG + RK A + + ++ E P LSGGN QK+++ R Sbjct: 380 LTARGCFTRGPF--LDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFY 437 Query: 419 TRPQFLILDEPTRGIDVGAHAEI-IRLIETLCADGLALLVISSELEELVGYADRVIIM 475 +P ++ + PT+G+D+ A E+ RL+E G +L++S +L E++ ADRV +M Sbjct: 438 RKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEVLALADRVAVM 493 Score = 80.1 bits (196), Expect = 2e-19 Identities = 66/243 (27%), Positives = 114/243 (46%), Gaps = 16/243 (6%) Query: 253 RAGRTLLSD-KPVAAFKNYGKK-GTIAP---FDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 R GR L D PV + GK G + L++ PG I L G G+G++ ++ Sbjct: 22 RTGRALRHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILS 81 Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367 G D+G + G+ RSP A GIG + ++ + +V EN++L Sbjct: 82 GRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFM---LVDSMTVAENVLLGQSG-- 136 Query: 368 GWLRPISRKEQ-QEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426 WL P+ E+A R+ G+ + + LS G +Q+V + + L + LIL Sbjct: 137 AWLSPVHMSRVVAELAARY----GLDIDPAARVCD-LSMGERQRVEILKLLYRDSRVLIL 191 Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486 DEPT + G ++ + + +G A++ IS +++E++ AD + I+R + V E Sbjct: 192 DEPTAVLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHE 251 Query: 487 AEL 489 +E+ Sbjct: 252 SEV 254 Score = 65.9 bits (159), Expect = 3e-15 Identities = 54/240 (22%), Positives = 110/240 (45%), Gaps = 12/240 (5%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L +GL+ G+K L F +R+GE+ A+ G G G+ L++ +TG+ G + L Sbjct: 284 VLHVDGLAG--DGLKGLS---FEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVEL 338 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLP---NMSVADNLFIGREP--KRFGLLRRKEME 123 G T +Q G+ + ++ L ++ + DN + R L RK + Sbjct: 339 LGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSAD 398 Query: 124 KRATELMASYGFSLDVRE-PLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVE 182 A +++A Y E P S Q + + R +++ + PT LD E Sbjct: 399 AAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATE 458 Query: 183 LLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242 ++ + ++R ++ V+ L++V ++DR+ V+ G F+G + + +++ + +M+ Sbjct: 459 EVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMM 517 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: 599 Number of extensions: 35 Number of successful extensions: 8 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: 524 Length adjustment: 35 Effective length of query: 465 Effective length of database: 489 Effective search space: 227385 Effective search space used: 227385 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