Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 282 bits (721), Expect = 1e-80 Identities = 161/368 (43%), Positives = 224/368 (60%), Gaps = 21/368 (5%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 + DL+ RFG + L+LDI EFLVL+G SGCGKST L +AGL+ T G I+I Sbjct: 13 VSARDLSVRFGAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQIWIN 72 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 +++ +R P++R +AMVFQ YALYP MTVR N+ FGL + AE D+ V E A L Sbjct: 73 DENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNK-VPKAEADKLVDEAARVLQ 131 Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183 + +LLDR+P ELSGGQ+QRVA+GRA+VR +VFL DEPLSNLDAKLRAE+R EL+ L + Sbjct: 132 LEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVELKRLHQE 191 Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243 L T +YVTH+Q EA+T+ADRIAVM DG +QQ+ SP E Y P N +VA+F+G P +N V Sbjct: 192 LGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNFV 251 Query: 244 RGTRSESTFV-GEHFSYPLDE-DVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHDL 301 G +ES + E F LD+ ++ + + +G+RPE + A+A Sbjct: 252 NGVVTESGAIQTEDFELALDQCNLASTPAPGTEVEIGIRPEHVHPANAG---------GF 302 Query: 302 QMDVTVVEPHGDQNVL--HLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLF 359 +DV +VE G + ++ + + DD + GD+V + + P +F Sbjct: 303 MLDVGMVELLGSERLIWGKVGNTSIVMRDDPDTTIRS-------GDQVRINLKPGAFSVF 355 Query: 360 DAETGTAV 367 A+TG + Sbjct: 356 SAKTGLRI 363 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: 329 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 363 Length adjustment: 30 Effective length of query: 353 Effective length of database: 333 Effective search space: 117549 Effective search space used: 117549 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