Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter
Query= SwissProt::P37388 (513 letters) >FitnessBrowser__HerbieS:HSERO_RS22465 Length = 518 Score = 546 bits (1407), Expect = e-160 Identities = 277/502 (55%), Positives = 377/502 (75%), Gaps = 3/502 (0%) Query: 3 YLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGE 62 YLLEMK I K+FG V+A++ + +++ GE V LCGENG+GKSTLMK+L G+YPHG++EGE Sbjct: 4 YLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEGE 63 Query: 63 IIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEIT-HNGIMDYDLMTL 121 I++ G+ +QA +RDTE GI IIHQEL LV EL+V ENIF+G+EIT G M+Y M Sbjct: 64 ILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPAMYR 123 Query: 122 RCQKLLAQVSL-SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180 R ++L+ ++++ I+ V G G QQLVEIAKALNK RLLILDEP++SLT E + Sbjct: 124 RAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIGV 183 Query: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 240 LL II+DL+ G+AC+YISHKL+EV + DTI VIRDG+HI T M D IIT MVG Sbjct: 184 LLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMVG 243 Query: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300 RE+TA+YP H G+ +L ++T + N KRV+DVSFS++RGEILGIAGLVGAGR Sbjct: 244 REITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVGAGR 303 Query: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360 TE + +FG + G++EG++ ++GK D + ++I +G+ MVPEDRK GIVP + VG+N Sbjct: 304 TELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPDLDVGQN 363 Query: 361 ITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCL 420 ITL LN+F+ G S++D +AE K I + I +++VKT++P L I LSGGNQQKA+LA+ L Sbjct: 364 ITLTVLNRFSRG-SRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAVLAKML 422 Query: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480 L P++LILDEPTRG+D+GAK EIY+LI++L + G+A+I++SSEL EVLG+SDRVLV+ E Sbjct: 423 LAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRVLVIGE 482 Query: 481 GKLKANLINHNLTQEQVMEAAL 502 G+L+ + +N NL+QE V+ AA+ Sbjct: 483 GRLRGDFVNDNLSQETVLAAAI 504 Score = 89.7 bits (221), Expect = 2e-22 Identities = 62/237 (26%), Positives = 119/237 (50%), Gaps = 7/237 (2%) Query: 18 KAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEEIQASHIRD 77 K +D+V + GEI+ + G G+G++ L+ + G Y G YEG+++ G+ S Sbjct: 278 KRVDDVSFSVRRGEILGIAGLVGAGRTELVSAIFGAY-RGRYEGQVLLEGKPADTSSPLK 336 Query: 78 TERKGIAIIHQEL---ALVKELTVLENIFLG--NEITHNGIMDYDLMTLRCQKLLAQVSL 132 + R+G+ ++ ++ +V +L V +NI L N + +D Q + ++ + Sbjct: 337 SIRRGLCMVPEDRKHHGIVPDLDVGQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRV 396 Query: 133 -SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQH 191 + +P + L G QQ +AK L Q ++LILDEPT + + + +I +L + Sbjct: 397 KTATPFLPITSLSGGNQQKAVLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKA 456 Query: 192 GIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRELTALYP 248 G+A I +S +L EV +SD + VI +G+ G +S++ ++ + + + P Sbjct: 457 GLAIIMVSSELAEVLGVSDRVLVIGEGRLRGDFVNDNLSQETVLAAAINQPVPQATP 513 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: 750 Number of extensions: 35 Number of successful extensions: 9 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: 513 Length of database: 518 Length adjustment: 35 Effective length of query: 478 Effective length of database: 483 Effective search space: 230874 Effective search space used: 230874 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