Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 262 bits (670), Expect = 2e-74 Identities = 171/486 (35%), Positives = 260/486 (53%), Gaps = 21/486 (4%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P++ L I K+F VRA + L G + AL+GENGAGKSTLM ILSG D G Sbjct: 33 PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTG-II 91 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 H+DG+ V+ P+ A G+ ++YQ L +++VAEN+ LG Q ++ M R Sbjct: 92 HVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLG---QSGAWLSPVHMSRVV 148 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 A AR G D PAA V LS+ +RQ VEI + ++ ++R+L++DEPT L+ ET++LF Sbjct: 149 AELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFE 208 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL-SQAALVKMMVGRD 250 + ++ G AI++ISH+M E+ LAD + +LR G V + + +A L MVGR+ Sbjct: 209 ALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGRE 268 Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310 + + + +E + D G +KG SF++R GEV +AG+ G G+ EL V Sbjct: 269 V---ILEVAAEPLEPGDRVLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECV 325 Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370 G GEV + P G G+AY+ EDR QGL S+ Sbjct: 326 TGLRRPAEGEVELLGIPWRQFFTKAPRQG-------GLAYIPEDR--QGLATCLSLDLVD 376 Query: 371 NLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 429 N ++ AR G L+R +A + + ++ A+ +LSGGN QK+++ R Sbjct: 377 NFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREF 436 Query: 430 EIQPRVLILDEPTRGVDIGAKSEIY-RLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488 +P +++ + PT+G+DI A E++ RL+ + +GV L++S +L EV+ L DRV VM Sbjct: 437 YRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAGV--LLVSGDLNEVLALADRVAVMY 494 Query: 489 EGTLAG 494 G G Sbjct: 495 RGCFIG 500 Score = 72.4 bits (176), Expect = 4e-17 Identities = 58/223 (26%), Positives = 103/223 (46%), Gaps = 17/223 (7%) Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQA 343 + D+ G + L G GAG++ L ++ G A+ G + + A + P+ A Sbjct: 54 TLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEA-------VRFRSPKDA 106 Query: 344 IDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGI 403 + AGI + + L +V EN+ L+ + L ++R A +D Sbjct: 107 LKAGIGMVYQHFMLVD---SMTVAENV-LLGQSGAWLSPVHMSRVVAELAARYGLDI--- 159 Query: 404 RVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQS 463 V LS G +Q+V + +LL RVLILDEPT + G +++ ++ +A++ Sbjct: 160 ---DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAEN 216 Query: 464 GVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQ 506 G AI+ IS ++ EV+ L D + ++R G + E + E + Sbjct: 217 GKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAE 259 Score = 63.5 bits (153), Expect = 2e-14 Identities = 64/236 (27%), Positives = 111/236 (47%), Gaps = 17/236 (7%) Query: 29 LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88 L+ + GEV A+ G G G+ L++ ++G GE + G + ++ R Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGL-RRPAEGEVELLGIPWRQFFTKAPRQ 353 Query: 89 LGVAVIYQE---LSLAPNLSVAENIYLGRALQRRGLVARGDMV-RACAPTLAR-LGADFS 143 G+A I ++ L+ +L + +N L RG RG + R A AR + A+++ Sbjct: 354 GGLAYIPEDRQGLATCLSLDLVDNFLL----TARGCFTRGPFLDRKSADAAARDILAEYN 409 Query: 144 -----PAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRG 198 A SLS Q + + R + + ++V + PT L T+ ++A + ++R Sbjct: 410 VQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRS 469 Query: 199 EGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQA-ALVKMMVGRDLSG 253 +L +S + E+ LADRV V+ GCF+G LDR+ ++ A+ MM G G Sbjct: 470 HA-GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVSCEG 524 Lambda K H 0.320 0.136 0.382 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: 655 Number of extensions: 36 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: 540 Length of database: 524 Length adjustment: 35 Effective length of query: 505 Effective length of database: 489 Effective search space: 246945 Effective search space used: 246945 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