Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 110 bits (274), Expect = 8e-29 Identities = 70/213 (32%), Positives = 120/213 (56%), Gaps = 6/213 (2%) Query: 12 KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71 K+ VKA+D ++ E+ GE + L+G++G GK+TL + I +P G+++F G+ + Sbjct: 328 KTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENITHI 387 Query: 72 SPNDARSL--GIETIYQD--LALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLDS 127 R L I+ I+QD +L P L I +I +V +K++ N + ++ +LLD Sbjct: 388 GKTALRKLRKDIQIIFQDPYASLNPKLSIGQSILEPLQV-HKLYRNDSERKQKVLELLDK 446 Query: 128 LQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNL 187 + ++ N SGGQRQ V +ARA+ K I+ DE +AL V +VL L ++L Sbjct: 447 VGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLIKDL 506 Query: 188 KKK-GLGVLIITHNIIQGYEVADRIYVLDRGKI 219 + + GL + I+H++ ++DRI V+++GKI Sbjct: 507 QSEFGLTYIFISHDLAVVKHISDRILVMNKGKI 539 Score = 84.3 bits (207), Expect = 5e-21 Identities = 63/219 (28%), Positives = 114/219 (52%), Gaps = 22/219 (10%) Query: 18 KALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDR----GDLVFEGKKVIFNSP 73 KA+ +S ++ KG V+ ++G++G+GKS I H G++ FE ++ S Sbjct: 21 KAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLSS 80 Query: 74 NDARSLG---IETIYQD--LALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK----L 124 N+ R + I I+Q+ +L P Y +V I L++K E+KK L Sbjct: 81 NEIRQIRGNQISMIFQEPMTSLNPVFTCGY------QVAEAIMLHRKVDQAEAKKHTIAL 134 Query: 125 LDSLQIRIPD--INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 + +Q+ P+ +SGGQ+Q V +A A+ K+++ DEPT AL V + +L+ Sbjct: 135 FNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQ 194 Query: 183 LARNLK-KKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 L LK ++ + ++ I+H++ E+AD + V+ +G+I+ Sbjct: 195 LLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIV 233 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: 282 Number of extensions: 16 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: 568 Length adjustment: 30 Effective length of query: 221 Effective length of database: 538 Effective search space: 118898 Effective search space used: 118898 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: 50 (23.9 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