Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= SwissProt::P37388 (513 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 542 bits (1397), Expect = e-158 Identities = 278/501 (55%), Positives = 364/501 (72%), Gaps = 3/501 (0%) Query: 4 LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 L EM+ I K+FG VKA+D + LRL AGE + LCGENG+GKSTLMKVL G+YPHGS++GEI Sbjct: 7 LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66 Query: 64 IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITH-NGIMDYDLMTLR 122 ++ G+ ++A +RD+ER GI IIHQEL LV +L+V ENIFLG+EIT G MDYD M + Sbjct: 67 LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAK 126 Query: 123 CQKLLAQVSL-SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSIL 181 LL ++ L ++ G G QQL EIAKAL KQ +LLILDEPT+SLT ET +L Sbjct: 127 ADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVL 186 Query: 182 LDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGR 241 L I+ DL++ G+ACIYISHKL+EV+ + DT+CVIRDG+HI T+ + D +IT+MVGR Sbjct: 187 LGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGR 246 Query: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301 +L LYP H G+ I H T PVN KRV+DVSF L+RGEILGIAGLVGAGRT Sbjct: 247 KLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRT 306 Query: 302 ETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNI 361 E + +FG + G+ +++++G+ + IR+ AI G+ MVPEDRKR GIVP++ VG NI Sbjct: 307 ELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNI 366 Query: 362 TLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLL 421 TLA L+ + +D E I I + +VKT+SP L I RLSGGNQQKA+LA+ LL Sbjct: 367 TLATLDHYAHA-GHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLL 425 Query: 422 LNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEG 481 P++LILDEPTRG+D+GAK EIY+LI +L QG+A++++SSE+PEVLG++DRVLVM EG Sbjct: 426 ARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEG 485 Query: 482 KLKANLINHNLTQEQVMEAAL 502 +L+ + N LTQEQV+ AA+ Sbjct: 486 RLRGDFPNQGLTQEQVLAAAI 506 Lambda K H 0.319 0.137 0.391 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: 745 Number of extensions: 26 Number of successful extensions: 8 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: 513 Length of database: 513 Length adjustment: 35 Effective length of query: 478 Effective length of database: 478 Effective search space: 228484 Effective search space used: 228484 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