Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 258 bits (659), Expect = 4e-73 Identities = 178/500 (35%), Positives = 257/500 (51%), Gaps = 25/500 (5%) Query: 4 MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63 M D+ T L L I K +PG A +++L+ GE+HAL+GENGAGKSTLMKI+ G Sbjct: 1 MPDSQTAR--LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVT 58 Query: 64 TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVA 123 D GE H G+RV + P AR+ G+ +++Q SL LSVAENI L L A Sbjct: 59 QPD-AGEIHWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALA-------LGA 110 Query: 124 RGDMVRACAPTLA----RLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTT 179 + + P + R G P V SLSI +RQ VEI R + + R+L++DEPT+ Sbjct: 111 KAGTPKQLEPKIREVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTS 170 Query: 180 PLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239 L+ E D LF +R+L EG +IL+ISH++ E+ L TVLR G G A S Sbjct: 171 VLTPQEADELFVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSD 230 Query: 240 AALVKMMVG--RDLSGFYTKTHGQAVEREVMLSVRDVAD--GRRVKGCSFDLRAGEVLGL 295 L ++MVG L Y K+ G+A V AD G +K ++RAGE++G+ Sbjct: 231 LELARLMVGDAEGLEAEYPKSEGRAPFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGI 290 Query: 296 AGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDR 355 AG+ G G+ EL L+ G + G P R G+A++ +R Sbjct: 291 AGVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRH----GMAFVPAER 346 Query: 356 KLQGLFLDQSVHENINLIVAARDA--LGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVG 413 G S+ +N L+ A + + G + R R + I ++ AQ Sbjct: 347 LGHGAVPSMSLADN-GLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAA 405 Query: 414 ALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSE 473 +LSGGN QK +L R + QP++LI PT GVD+GA + I+R + L +G AIL+IS + Sbjct: 406 SLSGGNLQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISED 465 Query: 474 LPEVVGLCDRVLVMREGTLA 493 L E+ + DR+ + +G L+ Sbjct: 466 LEELFQISDRIAALSDGRLS 485 Score = 79.0 bits (193), Expect = 4e-19 Identities = 74/236 (31%), Positives = 109/236 (46%), Gaps = 18/236 (7%) Query: 287 LRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDA 346 ++ GE+ L G GAG++ L ++++G GE+ G VT+ P QA + Sbjct: 31 IQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIH-----WQGERVTMR--DPAQARER 83 Query: 347 GIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVA 406 GI + + L F SV ENI L ALG + E G+ + Sbjct: 84 GIGMVFQHFSL---FETLSVAENIAL------ALGAKAGTPKQLEPKIREVSQRYGMPLE 134 Query: 407 HAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVA 466 ++ V +LS G +Q+V + R L R+LILDEPT + E++ + LA G + Sbjct: 135 PQRL-VHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCS 193 Query: 467 ILMISSELPEVVGLCDRVLVMREGTLAGEVRPAG-SAAETQERIIALATGAAAAAP 521 IL IS +L EV LC V+R G ++GE PA S E ++ A G A P Sbjct: 194 ILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAEGLEAEYP 249 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: 633 Number of extensions: 31 Number of successful extensions: 8 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: 518 Length adjustment: 35 Effective length of query: 505 Effective length of database: 483 Effective search space: 243915 Effective search space used: 243915 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