Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 127 bits (318), Expect = 6e-34 Identities = 72/216 (33%), Positives = 122/216 (56%), Gaps = 1/216 (0%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 L + K+F VKALD +S + G+V AL+G+NGAGKSTL+KI+ G + P G L Sbjct: 16 LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKL 124 + + F S D+ G+ I+Q+L L+P++ + N+FL + +N+ + +++ Sbjct: 76 ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALAC 135 Query: 125 LDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELA 184 L L I D KV LS GQRQ V +A+A+ A +I DEPT++LS E +++ + Sbjct: 136 LKGLADEI-DPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 185 RNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 L+ +G VL ++H + + + + + + V G+ + Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYV 230 Score = 101 bits (252), Expect = 3e-26 Identities = 56/220 (25%), Positives = 118/220 (53%), Gaps = 6/220 (2%) Query: 23 VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82 VS E++KGE++ L G GAG++ L++++SG + G L G ++ SP DA + GI Sbjct: 283 VSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGIL 342 Query: 83 TIYQDL---ALIPDLPIYYNIFLAREVTNKIF---LNKKKMMEESKKLLDSLQIRIPDIN 136 +D ++P + NI ++ + F L + +++ + +L+++ P+ Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAA 402 Query: 137 MKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGVLI 196 K+ LSGG +Q + R + K++L+DEPT + + ++ ++ NL +G+ V++ Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIV 462 Query: 197 ITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEV 236 ++ ++++ ++DRI VL G + +E+ N + ++ Sbjct: 463 VSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQL 502 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: 260 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: 514 Length adjustment: 29 Effective length of query: 222 Effective length of database: 485 Effective search space: 107670 Effective search space used: 107670 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