Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 157 bits (396), Expect = 5e-43 Identities = 82/224 (36%), Positives = 138/224 (61%), Gaps = 1/224 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LL IR + K+F V+ALDGV + GE+ ALLG+NGAGKSTLIK ++G ++ D G + Sbjct: 12 LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTL 71 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 EG+ + +A+ L I T+YQ++ L+P+L + N+FL R+ +++ M ++ Sbjct: 72 EGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRARA 131 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 +L + + D+ + S +Q VA+ARAV SAK++++DEPTA+L E + ++ Sbjct: 132 VLIPYGLTL-DVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKV 190 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEE 227 R L+ +G+G++ +TH + Q Y + DRI VL G+++ ++ E Sbjct: 191 MRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAE 234 Score = 88.6 bits (218), Expect = 2e-22 Identities = 55/233 (23%), Positives = 112/233 (48%), Gaps = 5/233 (2%) Query: 12 KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71 + +G ++++ ++I GEVV L G G+G++ +++ G + DRG+ +G+ V Sbjct: 275 RGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLR 334 Query: 72 SPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKIF--LNKKKMMEESKKLLD 126 P DA LG +D ++ L + NI LA + + + + E + + + Sbjct: 335 GPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLRPIPRCRQEEIADRFIR 394 Query: 127 SLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARN 186 L IR P ++ LSGG +Q +AR + +++++DEPT + V +++ L Sbjct: 395 LLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIER 454 Query: 187 LKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTS 239 L G+ +L+++ + + + R+ VL + + + E V+ I + S Sbjct: 455 LCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAAIAS 507 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: 248 Number of extensions: 8 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: 516 Length adjustment: 29 Effective length of query: 222 Effective length of database: 487 Effective search space: 108114 Effective search space used: 108114 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