Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 142 bits (359), Expect = 1e-38 Identities = 80/238 (33%), Positives = 133/238 (55%), Gaps = 2/238 (0%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 MS +E R+V K FG V+ L GV + G V LLG+NGAGKSTL+KI++GY P G+ Sbjct: 1 MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60 Query: 61 LVFEGK-KVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMME 119 +V +G + A + GI I+Q+ L DL I NIFL E+ +FL+ K M E Sbjct: 61 VVVDGAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMRE 120 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 ++++ L + + + D + +V L ++Q V +ARA+ +A++++MDEPTA L+ E + Sbjct: 121 KTREALAKVGLPL-DPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 + L LK G+ ++ I+H + + D + V+ G ++ + ++ +M Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLM 237 Score = 84.7 bits (208), Expect = 3e-21 Identities = 53/222 (23%), Positives = 109/222 (49%), Gaps = 14/222 (6%) Query: 21 DGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLG 80 +GV E+ +GE++ G GAG++ L + + G G + G+ V SP DA G Sbjct: 272 EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHG 331 Query: 81 IETIYQD---------LALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLDSLQIR 131 + + +D L P+L + +A E K +L+ ++ + IR Sbjct: 332 LTYLSEDRKGKGLHVHFGLRPNLTL-----MALERYAKPWLDPAAEQAALREAVQEFGIR 386 Query: 132 IPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKG 191 + ++ +LSGG +Q +A+A+ ++ ++++DEPT + V R++ L + L ++G Sbjct: 387 TGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQG 446 Query: 192 LGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233 L V++I+ +++ + R+ V+ G++ ++ EE+ Sbjct: 447 LAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEEL 488 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: 227 Number of extensions: 12 Number of successful extensions: 5 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: 496 Length adjustment: 29 Effective length of query: 222 Effective length of database: 467 Effective search space: 103674 Effective search space used: 103674 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