Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 135 bits (339), Expect = 2e-36 Identities = 73/218 (33%), Positives = 130/218 (59%), Gaps = 5/218 (2%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L++ +HK F + L V + + GE+ AL+G NGAGKSTLIK+++G + G + Sbjct: 18 VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAR----EVTNKIFLNKKKMME 119 G+ V +SP A+ LGI T+YQ++ L P+L + NIF R + ++ + + Sbjct: 78 GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQ 137 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 ++ L+ + ++I D+ + + +Q VA+ARA+ ++++++DEPT++L E +K Sbjct: 138 RARDLVARIGLQI-DVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQK 196 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRG 217 + E+ R L+ +GL ++ +TH + Q Y V+DRI VL G Sbjct: 197 LFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNG 234 Score = 97.4 bits (241), Expect = 5e-25 Identities = 61/214 (28%), Positives = 115/214 (53%), Gaps = 6/214 (2%) Query: 12 KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71 + G L + ++I GEVV L G G+G++ L +++ G +PDRG L +G+ V F Sbjct: 283 EGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFA 342 Query: 72 SPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKI--FLNKKKMMEESKKLLD 126 +P DA G+ ++ ++ +L + NI LA + + FL++ + E +++ + Sbjct: 343 NPMDAIRHGLALCPEERKTDGIVAELSVRENIALALQARMGVGKFLSRSEQTELAERYVK 402 Query: 127 SLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARN 186 L I+ ++ + LSGG +Q +AR + +++++DEPT + V +++++ Sbjct: 403 LLGIKTETVDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILR 462 Query: 187 LKKKGLGVLIITHNIIQGYEVADRIYVL-DRGKI 219 L + G+ VL I+ + + VA RI VL DR K+ Sbjct: 463 LAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRKV 496 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: 241 Number of extensions: 12 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: 517 Length adjustment: 29 Effective length of query: 222 Effective length of database: 488 Effective search space: 108336 Effective search space used: 108336 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