Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate Ac3H11_2431 ABC transporter ATP-binding protein
Query= SwissProt::P37388 (513 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2431 Length = 514 Score = 263 bits (671), Expect = 1e-74 Identities = 177/522 (33%), Positives = 264/522 (50%), Gaps = 24/522 (4%) Query: 1 MPYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYE 60 M +L + +ITK FG + A D++ L L GE+++L GENG+GKSTLM +L G Y + E Sbjct: 1 MSNVLRLSHITKRFGKLVANDSISLTLARGEVLALLGENGAGKSTLMSILFGHYV--ADE 58 Query: 61 GEIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMT 120 G I G+ + R GI ++HQ L LTVL+N+ LG+E Sbjct: 59 GSIEVFGQPLPPGQPRAALAAGIGMVHQHFTLADNLTVLDNVLLGSEPLWQPFSRRSEAR 118 Query: 121 LRCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180 + + Q L +SPD +VG L +G++Q VEI KAL + +LILDEPTA LT QE+ Sbjct: 119 AKLLAVSQQFGLPVSPDAKVGSLSVGERQRVEILKALYRGAHILILDEPTAVLTPQESEA 178 Query: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 240 L D + + G++ I+ISHKL EV +S + V+R G+ + A G ++ + MVG Sbjct: 179 LFDTLAQMVAQGLSIIFISHKLGEVLRVSHRVAVLRQGKLVAEAPAQGTTQGQLAQWMVG 238 Query: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300 + A G+ I + +++ P R R+NDVS +L+ GEI+ IAG+ G G+ Sbjct: 239 HAIEAAERRPAQNVGEPICTLSNVST-APAGR--DRLNDVSLTLRAGEIVAIAGVSGNGQ 295 Query: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360 L GV G++ + G + R ++QG+A +PEDR G+V + V +N Sbjct: 296 VALADVLCGV-RAATTGQVTLRGAPLQARPA-WLVSQGVARIPEDRHAVGVVGDLPVWEN 353 Query: 361 ITLAAL------NKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKA 414 L + + AA Q + V+ D LSGGN QK Sbjct: 354 AVSERLRGPWFAHPWFRAFWVKRRAARQHA-QRVAETFDVRGGGADAPARSLSGGNMQKL 412 Query: 415 ILARCLLLN----------PRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSE 464 IL R L+ P++++ +PT G+DIGA + + + G AV++IS + Sbjct: 413 ILGRALMPPQDAAGNSAPVPQLIVAHQPTWGLDIGAVMFVQQQLINARDSGAAVLLISDD 472 Query: 465 LPEVLGLSDRVLVMHEGKLKANLINHNLTQEQVMEAALRSEH 506 L EVL L DRV VMH+G+L L T+E + A + H Sbjct: 473 LDEVLALGDRVAVMHDGRLSEALPAEGWTREAIGLAMAGAAH 514 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: 595 Number of extensions: 32 Number of successful extensions: 11 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: 514 Length adjustment: 35 Effective length of query: 478 Effective length of database: 479 Effective search space: 228962 Effective search space used: 228962 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