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 HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 383 bits (984), Expect = e-111 Identities = 212/504 (42%), Positives = 317/504 (62%), Gaps = 6/504 (1%) Query: 9 VTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTG 68 V S + P ++ +R + + FPGV ALDN L G V AL+GENGAGKSTL+KIL+G Sbjct: 12 VAASSSSSVP-VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSG 70 Query: 69 IYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRT 128 +Y+ + G+IL+DG+P + A G+ IHQE L + L+ A+NIF+G PR Sbjct: 71 VYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGL 130 Query: 129 -IDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAA 187 ID +N ++ A+ + ++DP+ + +L++A++ +V IA+ALS ++R++IMDEPTAA Sbjct: 131 FIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAA 190 Query: 188 LSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQ 247 L+ EI +LFRI+R L+ QG I++ISHK DEL +IAD V R + ++T Sbjct: 191 LNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVM-RDGKYIATVPMQETSM 249 Query: 248 DEIVRMMVGR--DVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLI 305 D I+ MMVGR D E P D + VLE+R + RD+SFTLRKGEILG GL+ Sbjct: 250 DTIISMMVGRALDGEQRIPP-DTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLM 308 Query: 306 GAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPI 365 GAGR+E+++++FG +G++++ G + I SP DA+ GI Y+ E+R GLA+ M + Sbjct: 309 GAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDV 368 Query: 366 FQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGK 425 N+ L S+ R +R GF+ A+ Y +L ++ ++ LSGGNQQK+VI K Sbjct: 369 QANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428 Query: 426 WLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVM 485 WL ++ DEPT+GID+G+K+ ++ + LA +G +I+M+SSELPE++ MS RVLVM Sbjct: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488 Query: 486 KEGLSAGIFERAELSPEALVRAAT 509 EG G RA+ + E +++ AT Sbjct: 489 CEGRITGELARADATQEKIMQLAT 512 Score = 93.2 bits (230), Expect = 2e-23 Identities = 74/250 (29%), Positives = 121/250 (48%), Gaps = 20/250 (8%) Query: 273 PVLEIRNYSHR----TEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328 PV+ +RN R + F L GE+ + G GAG+S L + L G+ + SG ++ Sbjct: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERG-RHGLALPMPIFQNMTLPSLARTSRRGFLRAAN 387 L+G+ + I P+ A GI + +E + L+ IF + R R+ + Sbjct: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIF-------IGREPRKAMGLFID 133 Query: 388 EFALARKYAE-----RLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKG 442 E L R+ A RLD+ S PVG L+ QQ V I K L+ +V+I+DEPT Sbjct: 134 EDELNRQAAAIFARMRLDMDP---STPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAA 190 Query: 443 IDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPE 502 ++ A + I +L A+G+ I+ +S ++ E+ ++DRV VM++G E S + Sbjct: 191 LNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMD 250 Query: 503 ALVRAATGNA 512 ++ G A Sbjct: 251 TIISMMVGRA 260 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: 589 Number of extensions: 28 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: 520 Length adjustment: 35 Effective length of query: 477 Effective length of database: 485 Effective search space: 231345 Effective search space used: 231345 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