Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Length = 526 Score = 160 bits (405), Expect = 5e-44 Identities = 89/243 (36%), Positives = 149/243 (61%), Gaps = 2/243 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LLEI +V K F V AL V + + G V+AL+G+NGAGKSTL+KII+G ++PD G+L Sbjct: 32 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122 GK V+F +P A GI I+Q+L L+P + I NI++ RE N + ++ ++M + Sbjct: 92 RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 KLL+ L+I + D V NLS +RQ V +A+AV + + +++MDEPT+A++ E + Sbjct: 152 KLLERLRINL-DPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 210 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 + +LK++G G++ ITH + + + +AD + V G I ++ + + + + +M L Sbjct: 211 IIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 270 Query: 243 GKV 245 ++ Sbjct: 271 SQL 273 Score = 89.0 bits (219), Expect = 2e-22 Identities = 56/243 (23%), Positives = 122/243 (50%), Gaps = 9/243 (3%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LL +RD+ K G K VS +++ GE++ + G G+G++ + + I G D G++ Sbjct: 285 LLSVRDL-KLDGIFK---DVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRL 340 Query: 64 EGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLA--REVTNKIFLNKKKMM 118 +G+ V + P+ A G + +D L P L + N+ +A F+ +K + Sbjct: 341 DGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALR 400 Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 + + L+++ P + ++ LSGG +Q +AR + + +++++DEPT + V Sbjct: 401 ALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKA 460 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238 ++ L L +G+ V++I+ + + ++DR+ V+ G ++ + E E + ++ + Sbjct: 461 EIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLAS 520 Query: 239 SFA 241 + Sbjct: 521 GMS 523 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: 266 Number of extensions: 11 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: 526 Length adjustment: 29 Effective length of query: 222 Effective length of database: 497 Effective search space: 110334 Effective search space used: 110334 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