Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Length = 517 Score = 307 bits (786), Expect = 7e-88 Identities = 189/484 (39%), Positives = 282/484 (58%), Gaps = 17/484 (3%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 +L++ I KT+ L ++LT GEV AL GENGAGKSTL KI+ G A G+ Sbjct: 9 VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGL-VAPTTGQMR 66 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132 G+ + A +LG+ ++ QEL+L P LSVAEN++L G ++R + +A Sbjct: 67 FQGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAI 126 Query: 133 PTLARLGAD-FSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 +A++G D P V L I +Q+VEIAR + + +L++DEPT L+ E + LF Sbjct: 127 EAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 I +L+ G++I+YISHR+ E+ +A R+ VLRDG V A+ + LV +MVGR+L Sbjct: 187 QITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGREL 246 Query: 252 SGFYTKTHGQAVEREV---MLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELAR 308 H R++ L+V+ + +V+ SF++RAGE+ G++GL+GAGRTEL R Sbjct: 247 G-----EHIDMGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLR 301 Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368 L+FGAD G V + S +V++ + P A+ GIA +TEDRK +GL L QS+ Sbjct: 302 LIFGADTADSGTVAL---GASAQVVSIRS--PADAVGHGIALITEDRKGEGLLLTQSISA 356 Query: 369 NINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRL 428 NI L + G G +N I+ + IR + V LSGGNQQKV++ R Sbjct: 357 NIALGNMPVISSG-GFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRW 415 Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488 LE V++ DEPTRG+D+GAK +IY L+ L + G A++++SS+L E++ +CDR+ V+ Sbjct: 416 LERDCTVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLS 475 Query: 489 EGTL 492 G L Sbjct: 476 AGRL 479 Score = 85.5 bits (210), Expect = 4e-21 Identities = 71/248 (28%), Positives = 116/248 (46%), Gaps = 11/248 (4%) Query: 3 DMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGA 62 DM AP L ++ + ++ +R V AGE+ + G GAG++ L++++ GA Sbjct: 251 DMGPRKIGAPALTVKGLTRS----DKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGA 306 Query: 63 YTADPGGEC-HIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGR--AL 116 TAD G Q V I P A G+A+I ++ L S++ NI LG + Sbjct: 307 DTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVI 366 Query: 117 QRRGLVARGD-MVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMD 175 G V GD M A A SP V+ LS +Q V I R + + +++ D Sbjct: 367 SSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFD 426 Query: 176 EPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRA 235 EPT + ++AL+ +L +G A++ +S + E+ + DR+ VL G + T +R Sbjct: 427 EPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERD 486 Query: 236 HLSQAALV 243 +Q L+ Sbjct: 487 SWTQDDLL 494 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: 644 Number of extensions: 38 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 540 Length of database: 517 Length adjustment: 35 Effective length of query: 505 Effective length of database: 482 Effective search space: 243410 Effective search space used: 243410 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 Sep 17 2021. 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