Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 385 bits (989), Expect = e-111 Identities = 224/507 (44%), Positives = 317/507 (62%), Gaps = 15/507 (2%) Query: 25 LRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDILLD 82 +R + K F GV ALD L AGE L GENGAGKSTLMK+LSGVY S G+IL Sbjct: 10 MRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEILWQ 69 Query: 83 GKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAA 142 G+P+ R ++ GI IIHQEL L+ LS A+NIF+G E + G +D D + +A Sbjct: 70 GQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGR-MDYDAMYAKAD 128 Query: 143 AIFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 A+ + L D++ + P QQ+ EIAKAL+ +++LI+DEPT++L ++E L Sbjct: 129 ALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVLLG 188 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 I+ DL+ +GV +YISHK+DE+ ++ D V V+RDG++IAT PM E +DT+I++MVGR L Sbjct: 189 IVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGRKL 248 Query: 262 DG-EQRIPPDTSRNDVVLEVRGLN-------RGRAIRDVSFTLRKGEILGFAGLMGAGRT 313 + RI + + +V+ E R + + + DVSF LR+GEILG AGL+GAGRT Sbjct: 249 ENLYPRI--EHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRT 306 Query: 314 EVARAIFGADPLEAG-EIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANI 372 E+ AIFGA ++ E+ + G I+SPADA+ G+G + EDRK G+ + V NI Sbjct: 307 ELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNI 366 Query: 373 ALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLR 432 L+++ + G +D++ A + + + +KT S LSGGNQQK V+AK LL Sbjct: 367 TLATLDHYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLLA 426 Query: 433 DCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGR 492 +L DEPTRG+DVGAK+EIY+L+ LA QG AIV++SSE+PEVL M+ RVLVM EGR Sbjct: 427 RPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGR 486 Query: 493 ITGELARADATQEKIMQLATQRESAVA 519 + G+ TQE+++ A + A Sbjct: 487 LRGDFPNQGLTQEQVLAAAIDTSARAA 513 Lambda K H 0.320 0.135 0.372 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: 657 Number of extensions: 29 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 520 Length of database: 513 Length adjustment: 35 Effective length of query: 485 Effective length of database: 478 Effective search space: 231830 Effective search space used: 231830 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