Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate AO353_25420 AO353_25420 spermidine/putrescine ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25420 Length = 372 Score = 234 bits (597), Expect = 3e-66 Identities = 133/303 (43%), Positives = 184/303 (60%), Gaps = 15/303 (4%) Query: 4 IQLTDLTKRFGDT----VAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 + + + K +GD VA+ + LDI D EF L+GPSGCGK+T LRM+AG E PT G+ Sbjct: 12 VSIRAVRKVYGDPHSGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTQGE 71 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEE---EGYTSAERDERVV 116 I + G+++ R P R + VFQ YAL+PHMT+ +N+ FGLE + + A+ ERV Sbjct: 72 ILLYGENIADRPPYQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLSKAQIAERVR 131 Query: 117 EVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 176 E+ + + R+P +LSGGQQQRVAL RA+ P+V L+DEPLS LD KLR MR E Sbjct: 132 EMLALVQMERFATRRPTQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMREE 191 Query: 177 LQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236 L+ +Q + +T ++VTH+Q EA+TM+DRIAV+ +GE+QQV P + Y P N FVA+FIG Sbjct: 192 LKAIQAKTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFIG 251 Query: 237 EPMINLVRGTRSE-----STFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAP 291 E N + GT + + F G +PL V+ L VRPE + + A Sbjct: 252 E--TNFIEGTVTHVEAGLAWFAGP-AGHPLPAQPCSDVNVGATVALSVRPERLHLLPANT 308 Query: 292 DDA 294 D A Sbjct: 309 DGA 311 Lambda K H 0.317 0.135 0.386 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: 359 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 372 Length adjustment: 30 Effective length of query: 353 Effective length of database: 342 Effective search space: 120726 Effective search space used: 120726 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 (21.6 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