Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 150 bits (380), Expect = 4e-41 Identities = 84/220 (38%), Positives = 133/220 (60%), Gaps = 3/220 (1%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 ++ L E+R + K+F VKALD VS I GEV LLG+NGAGKS+L+K++ G + D G+ Sbjct: 7 ITPLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGE 66 Query: 61 LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI--FLNKKKMM 118 +G V SP D LGI I+Q+ +L+P L I NIFL RE +I ++ +M Sbjct: 67 FYHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMH 126 Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 E++++LD L + + V L Q+Q V +A+A+ +A+++++DEPTAALS E Sbjct: 127 AEARRILDILGMEV-STRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETE 185 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGK 218 K+ + LK G+ ++ I+H + + + + DRI +L G+ Sbjct: 186 KLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGR 225 Score = 89.7 bits (221), Expect = 1e-22 Identities = 65/244 (26%), Positives = 116/244 (47%), Gaps = 24/244 (9%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 L++R+V G + +++++ GE+V L G G+G+S + + + G +G++ Sbjct: 266 LDVRNVSADSG----IADINLQVRAGEIVGLAGLVGSGRSEVARAVFGADPIRQGEIYIF 321 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFL------------ 112 GK++ P+ AR LG ALIP+ + L R V + + L Sbjct: 322 GKRLT-GGPDRARELGA-------ALIPESRKSEGLALIRTVRDNLLLAGLRRAFPARWY 373 Query: 113 NKKKMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAAL 172 K +++ + L+I PD N + LSGG +Q + + + + AK+ + DEPT + Sbjct: 374 RADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIFDEPTRGI 433 Query: 173 SVVEARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEE 232 V ++ L +L K+G GVL+I+ + + V DR YV+ G+I E E Sbjct: 434 DVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHAEMTEER 493 Query: 233 ITEV 236 I ++ Sbjct: 494 ILQL 497 Lambda K H 0.318 0.137 0.371 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: 280 Number of extensions: 19 Number of successful extensions: 4 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: 251 Length of database: 502 Length adjustment: 29 Effective length of query: 222 Effective length of database: 473 Effective search space: 105006 Effective search space used: 105006 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: 49 (23.5 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