Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 320 bits (820), Expect = 8e-92 Identities = 201/492 (40%), Positives = 286/492 (58%), Gaps = 33/492 (6%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG---- 68 +LA + KT+ L +V L+ AGEV AL GENGAGKSTL K++SG G Sbjct: 16 VLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTY 74 Query: 69 -GECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDM 127 G+ + G R + A LGV ++ QEL+L P L+VAEN++L R G ++ + Sbjct: 75 RGQAYAPGSRGE------AERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRL 128 Query: 128 VRACAPTLARLGAD-FSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186 + +AR+G D P V L I +Q+VEIAR + + +L++DEPT L+ E Sbjct: 129 RQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREV 188 Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246 LF I +LR G+AI+YISHR+ E+ +A R+ VLRDG V S A LV +M Sbjct: 189 ALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLM 248 Query: 247 VGRDLSGFYTKTHGQAVEREV---MLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGR 303 VGR+L H R++ +L V + G +V+ SF++RAGE+ G++GL+GAGR Sbjct: 249 VGRELG-----EHIDLGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGR 303 Query: 304 TELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLD 363 TEL RL++GAD G + + P + + P+ A+ AGIA +TEDRK +GL L Sbjct: 304 TELLRLIYGADRADSGGIALGQPPQAVSI-----DSPKAAVRAGIALITEDRKGEGLLLT 358 Query: 364 QSVHENI---NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420 QS+ NI NL +R G L+ A + I + IR A AQ VG LSGGNQ Sbjct: 359 QSISANIALGNLGAVSR----AGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQ 414 Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480 QKV++ R LE +VL+ DEPTRG+D+GAK +IY L+ LA+ G A++++SS+L E++ + Sbjct: 415 QKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLI 474 Query: 481 CDRVLVMREGTL 492 CDR+ V+ G L Sbjct: 475 CDRIAVLSAGRL 486 Score = 90.9 bits (224), Expect = 1e-22 Identities = 74/249 (29%), Positives = 121/249 (48%), Gaps = 13/249 (5%) Query: 3 DMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGA 62 D+ APLL + +C+ +R+V AGE+ + G GAG++ L++++ GA Sbjct: 258 DLGRRQLGAPLLKVDKLCRG----DKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGA 313 Query: 63 YTADPGG-ECHIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGR--AL 116 AD GG Q V ID P++A G+A+I ++ L S++ NI LG A+ Sbjct: 314 DRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAV 373 Query: 117 QRRGLVARGDMVRACAPTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVM 174 R G V + +A A + S A V LS +Q V I R + + ++L+ Sbjct: 374 SRAG-VLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLF 432 Query: 175 DEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDR 234 DEPT + ++ L+ +L +G A++ +S + E+ + DR+ VL G + T R Sbjct: 433 DEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFAR 492 Query: 235 AHLSQAALV 243 H SQ L+ Sbjct: 493 DHWSQDQLL 501 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: 664 Number of extensions: 46 Number of successful extensions: 10 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: 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 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