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 AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 331 bits (848), Expect = 4e-95 Identities = 180/509 (35%), Positives = 303/509 (59%), Gaps = 15/509 (2%) Query: 9 VTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTG 68 +TD +P +L +RG+S+ F GV+ALD V + G + AL+GENGAGKSTL+K LTG Sbjct: 1 MTDPTPTASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTG 60 Query: 69 IYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRT 128 +Y+ + G + ++GR + A + ++QE L L+VAEN+FLG P RF Sbjct: 61 VYQRDAGTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPM-RFGL 119 Query: 129 IDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAAL 188 +D M R++A+L +D T L S+A + +VAIARA+ + A+++I+DEPTA+L Sbjct: 120 VDRGAMRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASL 179 Query: 189 SRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQD 248 +E+ LF+++R L+ +G I+F++H D++Y + D V R R + + P+ Sbjct: 180 DAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVL-RNGRLVGERRTAELPRL 238 Query: 249 EIVRMMVGRDVENVFPKI-------DVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGV 301 ++V MM+GR++E V +I + P++ R Y +R GE++G+ Sbjct: 239 DLVAMMLGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGL 298 Query: 302 YGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLAL 361 GL+G+GR+E ++ +FG+ + G+ ++GQ + + P+DAIR G + PE+R + G+ Sbjct: 299 AGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVG 358 Query: 362 PMPIFQNMTLPSLARTSRRGFLRA---ANEFALARKYAERLDLRAAALSVPVGTLSGGNQ 418 + + +N+ L A +R+G+LR + +A ++ LD+R P+ LSGGNQ Sbjct: 359 ALSVRENIIL---ALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQ 415 Query: 419 QKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGM 478 QK ++ +WLAT P+++ILDEPT+GID+G+ A + I L A+G+++++VSSEL EI+ Sbjct: 416 QKALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAY 475 Query: 479 SDRVLVMKEGLSAGIFERAELSPEALVRA 507 S RV+V+++ E++ + +V A Sbjct: 476 SRRVVVLRDRRHVAELRGGEVAVDRIVAA 504 Score = 85.1 bits (209), Expect = 5e-21 Identities = 72/250 (28%), Positives = 110/250 (44%), Gaps = 26/250 (10%) Query: 273 PVLEIRNYSHR----TEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328 P+L IR S + FT+R GEI + G GAG+S L ++L G+ + +G + Sbjct: 11 PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVT 70 Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANE 388 LEG+ I ++A R I V +E LP+L+ R Sbjct: 71 LEGRAIAPRGVEEAQRLHIGTVYQEVN--------------LLPNLSVAENLFLGRQPMR 116 Query: 389 FALARKYAERLDLRAAAL--------SVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPT 440 F L + A R RA + + P+G S QQ V I + + + KV+ILDEPT Sbjct: 117 FGLVDRGAMRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPT 176 Query: 441 KGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELS 500 +D A + + L + G+ I+ V+ L ++ + DR+ V++ G G AEL Sbjct: 177 ASLDAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELP 236 Query: 501 PEALVRAATG 510 LV G Sbjct: 237 RLDLVAMMLG 246 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: 658 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: 512 Length of database: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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