Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 377 bits (969), Expect = e-109 Identities = 224/519 (43%), Positives = 315/519 (60%), Gaps = 31/519 (5%) Query: 2 SATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDS--G 59 S I K F GV+ALDG+ + G+ GL GENGAGKSTL+K+L G Y S G Sbjct: 5 SCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDG 64 Query: 60 RVMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKR 119 ++ G +R S S AGI +IHQEL VP L+VAEN+ LG R R Sbjct: 65 EILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEIT-------RPGGR 117 Query: 120 FVRERLEAMGVALDPNAKLRKLSIA---------QRQMVEICKALLRNARVIALDEPTSS 170 + + A AL L +++A +Q+ EI KAL + A+++ LDEPTSS Sbjct: 118 MDYDAMYAKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSS 177 Query: 171 LSHRETEVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTR 230 L+ ETEVL +V DL+ A IYISH++DE+ +CD + RDGR IA+ P E + Sbjct: 178 LTSSETEVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHE-LDV 236 Query: 231 DTIVSEMVGREISDIYNYSARPLGEVRFAAKGIEGHALAQP-------ASFEVRRGEIVG 283 DT+++ MVGR++ ++Y +GEV F A+ P SF++RRGEI+G Sbjct: 237 DTLITLMVGRKLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILG 296 Query: 284 FFGLVGAGRSELMHLVYGA-DHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGI 342 GLVGAGR+EL+ ++GA K EL L+G+P+K+RS +AIR G+ + PEDRK GI Sbjct: 297 IAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGI 356 Query: 343 VAMATVSENINISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQ 402 V + V +NI ++ HY G +DR++E + I ++KT S I LSGGNQ Sbjct: 357 VPLLGVGDNITLATLDHYAHAG-HIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQ 415 Query: 403 QKAILSRWL-AEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVL 461 QKA+L++ L A P KV+ILDEPTRG+DVGAK EIY +I++LA +G AIV++SSE+PEVL Sbjct: 416 QKAVLAKMLLARP--KVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVL 473 Query: 462 GVSDRIVVMRQGRISGELTRKDATEQSVLSLALPQSSTA 500 G++DR++VM +GR+ G+ + T++ VL+ A+ S+ A Sbjct: 474 GMADRVLVMGEGRLRGDFPNQGLTQEQVLAAAIDTSARA 512 Lambda K H 0.320 0.136 0.385 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: 686 Number of extensions: 34 Number of successful extensions: 13 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: 512 Length of database: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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