Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_900177735.1:WP_085545256.1 Length = 503 Score = 152 bits (385), Expect = 1e-41 Identities = 81/231 (35%), Positives = 141/231 (61%), Gaps = 2/231 (0%) Query: 7 IRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGK 66 ++ + KSF +KA D + + + KGEV+ALLG+NGAGKSTL+ ++SG + PD G + G Sbjct: 1 MKGITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGT 60 Query: 67 KVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLD 126 ++ F SPNDA S GI ++Q L+P ++ N+ L +I L K K++ E + Sbjct: 61 RLSFRSPNDAISAGIGMVHQHFMLVPSQTVWENMVLGLPDLPQI-LPKGKIISEITAISK 119 Query: 127 SLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARN 186 + + D + LS G++Q V + + +Y +A+++++DEPTA L+ EAR + + Sbjct: 120 QYGLEV-DPEAIIWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKR 178 Query: 187 LKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 + ++G G++ I+H + + E++DR+ VL +GK+I +E + E+I E+M Sbjct: 179 MTEEGRGIIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEMM 229 Score = 97.4 bits (241), Expect = 5e-25 Identities = 65/240 (27%), Positives = 123/240 (51%), Gaps = 8/240 (3%) Query: 17 VKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDA 76 +KALD VS+E+ +G+++ L G G G++ L ++++G K G L+ +GK+V +SP + Sbjct: 263 LKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGLRKMTSGKLILKGKEVTDSSPREL 322 Query: 77 RSLGIETIYQD---LALIPDLPIYYNIFLAR----EVTNKIFLNKKKMMEESKKLLDSLQ 129 GI I D ++ ++ + N L R V + ++ K +++ + ++ + Sbjct: 323 IDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPVARGVLIDWKAVLKHALGIVKNFN 382 Query: 130 IRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKK 189 + P + V NLSGG Q + + R + K+++ PT L V R V E ++ Sbjct: 383 VDTPSVETPVRNLSGGNIQKLMLGRELSDIPKVLIAMNPTWGLDVAATRFVREQLLEERE 442 Query: 190 KGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEET-NVEEITEVMTSFALGKVNLG 248 KG + +I+ ++ + ++DRI V+ RGKI+ + T +E I +M + +V G Sbjct: 443 KGAAIFLISEDLDELMSLSDRIAVMYRGKIMGLVEDPNTFGIERIGMMMAGTRIEQVGGG 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: 278 Number of extensions: 14 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: 503 Length adjustment: 29 Effective length of query: 222 Effective length of database: 474 Effective search space: 105228 Effective search space used: 105228 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 24 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