Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 147 bits (372), Expect = 3e-40 Identities = 80/243 (32%), Positives = 139/243 (57%), Gaps = 2/243 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +LE+R + K+FGA +ALDG S+ + G V L+G+NGAGKSTLIK+++G H+PD G L+ Sbjct: 5 VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 +G+ SP LGI I+Q+ L + +F E L+++ E+ + Sbjct: 65 DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAAR 124 Query: 124 LLDS-LQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 LLD +R+P N + LS ++Q V + RA+ ++++ DEP+ AL E ++L Sbjct: 125 LLDDYFGLRLP-ANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 + + L+ GL ++ I+H + + + DR+ VL G+ + T++E+IT +M + + Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREV 243 Query: 243 GKV 245 G++ Sbjct: 244 GEL 246 Score = 102 bits (255), Expect = 1e-26 Identities = 70/242 (28%), Positives = 124/242 (51%), Gaps = 13/242 (5%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LL++R + G +A G+ +++ +GE+V L G G+G L++ + G PD G++ Sbjct: 258 LLDVRGL----GRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRL 313 Query: 64 EGKKVIFNSPNDARSLGI-----ETIYQDLALIPDLPIYYNIFLAR--EVTNKIFLNKKK 116 +G+ + SP +A + G+ E Q +AL DL + N LA L+ + Sbjct: 314 DGQPLSLRSPREAVAQGVALMPEERRRQGVAL--DLSVQENTTLAALSRFVRLGLLSPAR 371 Query: 117 MMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVE 176 + +L++ L+I+ + KV LSGG +Q VA+A+ + + L+DEP+ + V Sbjct: 372 ERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPSVGIDVGA 431 Query: 177 ARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEV 236 ++ L L K+G GVLI++ ++ + + DRI+V+ RG I E N + + V Sbjct: 432 KVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEANSDRLLAV 491 Query: 237 MT 238 T Sbjct: 492 AT 493 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: 231 Number of extensions: 11 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: 512 Length adjustment: 29 Effective length of query: 222 Effective length of database: 483 Effective search space: 107226 Effective search space used: 107226 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