Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 236 bits (601), Expect = 2e-66 Identities = 154/491 (31%), Positives = 256/491 (52%), Gaps = 24/491 (4%) Query: 11 DSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIY 70 DS+T A L++ GI++ +PG A D + +++ PG + AL+GENGAGKSTL+KI+ G+ Sbjct: 3 DSQT----ARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVT 58 Query: 71 RPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTID 130 +P+ GEI G T A + G+ + Q LF+ L+VAENI L + Sbjct: 59 QPDAGEIHWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAGTP--- 115 Query: 131 WQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSR 190 + + + + + ++P + LSI +R V I R L + R++I+DEPT+ L+ Sbjct: 116 -KQLEPKIREVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTP 174 Query: 191 KEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEI 250 +E D+LF +R L +G +ILFISHK +E+ + V R R + + E+ Sbjct: 175 QEADELFVTLRRLAAEGCSILFISHKLNEVRALCQSATVL-RAGRVSGECIPAECSDLEL 233 Query: 251 VRMMVG--RDVENVFPKIDVAIGGPVLEIRNYS-HRTE-----FRDISFTLRKGEILGVY 302 R+MVG +E +PK + P L + S H + +++ +R GEI+G+ Sbjct: 234 ARLMVGDAEGLEAEYPKSEGR--APFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIA 291 Query: 303 GLIGAGRSELSQSLFG---ITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGL 359 G+ G G+ EL L G + + ++ G ++ P R G+ +VP ER HG Sbjct: 292 GVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGA 351 Query: 360 ALPMPIFQNMTLPSLARTS--RRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGN 417 M + N L + +T +G +R A A + +R ++ P +LSGGN Sbjct: 352 VPSMSLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGN 411 Query: 418 QQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIG 477 QK ++G+ + PK++I PT G+D+G+ AA+H + EL G +I+++S +L E+ Sbjct: 412 LQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQ 471 Query: 478 MSDRVLVMKEG 488 +SDR+ + +G Sbjct: 472 ISDRIAALSDG 482 Score = 34.7 bits (78), Expect = 9e-06 Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 1/90 (1%) Query: 168 IARALSIEARIVIMDEPTAALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDF 227 + R + + +++I PT + + R + L++ G AIL IS +EL++I+D Sbjct: 417 LGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRI 476 Query: 228 VVFPRRSRRPVRGVSRKTPQDEIVRMMVGR 257 P R + P E+ R M G+ Sbjct: 477 AALSDGRLSPQRATASTCPV-EVGRWMAGQ 505 Lambda K H 0.320 0.137 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: 611 Number of extensions: 30 Number of successful extensions: 7 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: 512 Length of database: 518 Length adjustment: 35 Effective length of query: 477 Effective length of database: 483 Effective search space: 230391 Effective search space used: 230391 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