Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 144 bits (362), Expect = 5e-39 Identities = 79/239 (33%), Positives = 140/239 (58%), Gaps = 3/239 (1%) Query: 2 SDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGY--HKPDRG 59 S L E+R + KSFG VKALDG+ + + GE + L G+NGAGKSTL+K++SG H G Sbjct: 5 SCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDG 64 Query: 60 DLVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK-IFLNKKKMM 118 +++++G+ + S D+ GI I+Q+L L+P L + NIFL E+T ++ M Sbjct: 65 EILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMY 124 Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 ++ LL L + ++ + + GG +Q +A+A+ AK++++DEPT++L+ E Sbjct: 125 AKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETE 184 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 +L + +LK++G+ + I+H + + V D + V+ G+ I + E +V+ + +M Sbjct: 185 VLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLM 243 Score = 80.1 bits (196), Expect = 8e-20 Identities = 49/208 (23%), Positives = 107/208 (51%), Gaps = 6/208 (2%) Query: 18 KALDGVSMEINKGEVVALLGDNGAGKSTLIKIISG-YHKPDRGDLVFEGKKVIFNSPNDA 76 K +D VS ++ +GE++ + G GAG++ L+ I G Y +L EG+ + SP DA Sbjct: 280 KRVDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADA 339 Query: 77 RSLGIETIYQDL---ALIPDLPIYYNIFLAR--EVTNKIFLNKKKMMEESKKLLDSLQIR 131 G+ + +D ++P L + NI LA + +++++ + + + +++ Sbjct: 340 IRAGLGMVPEDRKRHGIVPLLGVGDNITLATLDHYAHAGHIDRQRELVAIEAQIAERRVK 399 Query: 132 IPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKG 191 + + LSGG +Q +A+ + K++++DEPT + V ++ L L +G Sbjct: 400 TASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQG 459 Query: 192 LGVLIITHNIIQGYEVADRIYVLDRGKI 219 + +++++ + + +ADR+ V+ G++ Sbjct: 460 VAIVLVSSEMPEVLGMADRVLVMGEGRL 487 Lambda K H 0.318 0.137 0.371 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: 233 Number of extensions: 10 Number of successful extensions: 6 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: 251 Length of database: 513 Length adjustment: 29 Effective length of query: 222 Effective length of database: 484 Effective search space: 107448 Effective search space used: 107448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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