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 Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Length = 517 Score = 287 bits (735), Expect = 6e-82 Identities = 174/496 (35%), Positives = 276/496 (55%), Gaps = 12/496 (2%) Query: 19 AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78 A+L + GI + + L + + L G V AL GENGAGKSTL KI+ G+ P G++ Sbjct: 8 AVLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMR 66 Query: 79 VDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138 GR S A + G+ + QE L L+VAEN+FL + P W + Sbjct: 67 FQGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHG----GWISRKQLR 122 Query: 139 KALLTALES----NIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEID 194 KA + A+ IDP + +L I + +V IAR L + ++I+DEPTA L+ +E++ Sbjct: 123 KAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVE 182 Query: 195 DLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMM 254 LF + L+ +G +I++ISH+ +EL +A V + V ++ +++V +M Sbjct: 183 MLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYN-SEQLVTLM 241 Query: 255 VGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQ 314 VGR++ IG P L ++ + + RD+SF +R GEI G+ GLIGAGR+EL + Sbjct: 242 VGRELGEHIDMGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLR 301 Query: 315 SLFGITKPLSGKMVL--EGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLP 372 +FG SG + L Q ++I SP DA+ GI + E+R GL L I N+ L Sbjct: 302 LIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALG 361 Query: 373 SLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPK 432 ++ S GF+ +E +LA++ + +R+++ + V LSGGNQQKVVIG+WL Sbjct: 362 NMPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCT 421 Query: 433 VIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAG 492 V++ DEPT+GID+G+K ++ + EL +G ++++VSS+L E++ + DR+ V+ G Sbjct: 422 VMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLID 481 Query: 493 IFERAELSPEALVRAA 508 FER + + L+ AA Sbjct: 482 TFERDSWTQDDLLAAA 497 Score = 84.3 bits (207), Expect = 9e-21 Identities = 67/222 (30%), Positives = 107/222 (48%), Gaps = 5/222 (2%) Query: 289 ISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIV 348 I TL +GE+L + G GAG+S LS+ + G+ P +G+M +G++ S A GI Sbjct: 27 IDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGRDYRPGSRSQAEELGIR 86 Query: 349 YVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSV 408 V +E L + + +N+ L +L S G++ A + ++ L A Sbjct: 87 MVMQELN---LLPTLSVAENLFLDNLP--SHGGWISRKQLRKAAIEAMAQVGLDAIDPDT 141 Query: 409 PVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMV 468 VG L G+QQ V I + L V+ILDEPT + + I+ L A G+SII + Sbjct: 142 LVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVSIIYI 201 Query: 469 SSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 S L E+ ++ R+ V+++G + A + E LV G Sbjct: 202 SHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVG 243 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: 629 Number of extensions: 34 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: 517 Length adjustment: 35 Effective length of query: 477 Effective length of database: 482 Effective search space: 229914 Effective search space used: 229914 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