Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 154 bits (389), Expect = 3e-42 Identities = 86/238 (36%), Positives = 150/238 (63%), Gaps = 4/238 (1%) Query: 2 SDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDL 61 S +L + + K+F V+ALDGVS+ I GEV AL+G+NGAGKSTL+K++ G H+PD G + Sbjct: 5 SPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQI 64 Query: 62 VFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIF--LNKKKMME 119 + + V+ + P DA++ GI I+Q+L+L +L + NI+L E+ K F ++ ++ Sbjct: 65 IVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLG-ELPRKRFGLVDWAELEA 123 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 ++ +L+ L++ + +V +LS +Q V +ARA+ AK ++ DEPTA+L+ E Sbjct: 124 KTNAILEKLKVGF-NAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVV 182 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 + E+ +L+++G+G+ I+H + + +++ DRI VL G+ ETN E +T++M Sbjct: 183 LFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMM 240 Score = 93.6 bits (231), Expect = 7e-24 Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 9/246 (3%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 LE+R + S G++ + V+ E+ +GEVV G GAG++ + + + G P G + + Sbjct: 261 LEVRGL--SCGSL--FEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLD 316 Query: 65 GKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKI--FLNKKKMME 119 G +V SP+DA GI + +D L+ + N+ L + K F+ + Sbjct: 317 GAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIA 376 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 + D L IR P V NLSGG +Q + + + + ++++DEPT + V + Sbjct: 377 IFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAE 436 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTS 239 + L R+L +G V++I+ + + VADRI + G+I+ EE E + ++ Sbjct: 437 IHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496 Query: 240 FALGKV 245 KV Sbjct: 497 LDTEKV 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: 271 Number of extensions: 13 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 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