Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 141 bits (356), Expect = 2e-38 Identities = 85/239 (35%), Positives = 139/239 (58%), Gaps = 10/239 (4%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LL++ V KSF V+ALD V + + GEV ALLG+NGAGKSTLIKI+S H D G + F Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 64 EGKKVIFNSPNDA----RSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMME 119 G+ + P DA + LGI TIYQ+ L P+L + N++L RE ++ ++ Sbjct: 63 AGQVL---DPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 Query: 120 ESKKLLDSLQIRI-PDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 +++ LL+ L + + PD V L+ ++Q V +A+A+ +A++I+MDEPTAALS E Sbjct: 120 DAQALLNDLGLPLNPD--APVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVD 177 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 ++ + LK + + V+ ++H + + + DR V+ G+ + + V ++ +M Sbjct: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLM 236 Score = 80.5 bits (197), Expect = 6e-20 Identities = 56/211 (26%), Positives = 98/211 (46%), Gaps = 20/211 (9%) Query: 23 VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82 VS GE+V L G GAG++ L ++I G G ++ + K + SP DA GI Sbjct: 278 VSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGI- 336 Query: 83 TIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLDS-------------LQ 129 L+P+ FL + + L K + + +D L+ Sbjct: 337 ------MLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLR 390 Query: 130 IRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKK 189 I++ D + LSGG +Q V + RA+ + K++++DEPT + + +V ++ +L Sbjct: 391 IKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLAD 450 Query: 190 KGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 G+ V++I+ + + V+DRI V G I+ Sbjct: 451 LGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 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: 264 Number of extensions: 13 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: 515 Length adjustment: 29 Effective length of query: 222 Effective length of database: 486 Effective search space: 107892 Effective search space used: 107892 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