Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 245 bits (625), Expect = 3e-69 Identities = 161/480 (33%), Positives = 248/480 (51%), Gaps = 9/480 (1%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDT--GEVRFSGAA 77 + K FG AL+ + +R+ GE L G NGAGKSTL+ +L+G+ + GE+ + G Sbjct: 13 IAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEILWQGQP 72 Query: 78 APSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLR-GGVIDWQAMRRDARALLD 136 + + RD+ R + ++Q ++ LSVAEN+F+ + R GG +D+ AM A ALL Sbjct: 73 LRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAKADALLQ 132 Query: 137 HWKI-DVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISE 195 + DV A +QL EIA+AL+ A+ +ILDEPT+ L E + L + + Sbjct: 133 ELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVLLGIVED 192 Query: 196 LQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG---ERGG 252 L+R GV ++ISH L EV +C V V+RD RHI + P+ L + LI M G E Sbjct: 193 LKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGRKLENLY 252 Query: 253 LAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAI 312 + A A A L+ + VSF ++RGE++G+ G +GRT + AI Sbjct: 253 PRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRTELVSAI 312 Query: 313 AGLRAAKRGT-ISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIAR 371 G K + ++G L ++ G+G VP+DR G+V V +N ++ Sbjct: 313 FGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNITLATLD 372 Query: 372 VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431 G ++ + I + P ++ LSGGNQQK V+A+ L P VL+ Sbjct: 373 HYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLLARPKVLI 432 Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490 L +PT GVDV +K + ++ + +G A+++VS E+ + L DRVLVM GR+ +FP Sbjct: 433 LDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGRLRGDFP 492 Score = 55.5 bits (132), Expect = 5e-12 Identities = 58/223 (26%), Positives = 96/223 (43%), Gaps = 7/223 (3%) Query: 30 LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG-EVRFSGAAAPSIADRDAWR 88 ++DVS ++ GE + G GAG++ LVS + G + E+ G + DA R Sbjct: 282 VDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIR 341 Query: 89 ERVACVYQHST---IIRDLSVAENLFINRQP--LRGGVIDWQAMRRDARALLDHWKIDVR 143 + V + I+ L V +N+ + G ID Q A + ++ Sbjct: 342 AGLGMVPEDRKRHGIVPLLGVGDNITLATLDHYAHAGHIDRQRELVAIEAQIAERRVKTA 401 Query: 144 EDARA-GDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVT 202 A LS +Q +A+ L + +ILDEPT +D ++R I EL +GV Sbjct: 402 SPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVA 461 Query: 203 FLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEA 245 + +S + EV + V V+ + R P L +EQ++ A Sbjct: 462 IVLVSSEMPEVLGMADRVLVMGEGRLRGDFPNQGLTQEQVLAA 504 Lambda K H 0.318 0.134 0.377 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: 636 Number of extensions: 35 Number of successful extensions: 11 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: 510 Length of database: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 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: 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