Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 320 bits (819), Expect = 5e-92 Identities = 185/364 (50%), Positives = 236/364 (64%), Gaps = 20/364 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA++TL+ V KVY + + AV S I+DGEF+VLVGPSGCGKST LRM+AGLE + Sbjct: 1 MAQVTLNSVRKVYPN----GVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 TEG L + DRV+N V DRDIAMVFQ+YALYPH +VR N+++GL+ P+ EI+Q+V Sbjct: 57 TEGTLEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRK-TPEAEIKQKV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E ML + + LDRKP QLSGGQ+QRVA+GRAIVRDP +FL DEPLSNLDAKLR +MR Sbjct: 116 AEAAKMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRI 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ LQ LGVT++YVTHDQ EAMTM DR+ VL+ G ++Q+GTP + YH P ++FVA F+ Sbjct: 176 EIKALQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFM 235 Query: 241 GEPSMNLFDGSL-SGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQR 299 G P MNL D ++ +G DG GA GA + LGIRPEDV + G Sbjct: 236 GAPPMNLLDATIANGQVTLPDGVS---MGALDTSAQGA--VKLGIRPEDVQL--VAEGGL 288 Query: 300 TFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFD 359 D E ++E G +H + G FT V+ G +S AI LFD Sbjct: 289 AIDVE--LIEELGAHRLLHGKL----GGQPFTIHVLKDIPVDPGTH-QISVDPAAICLFD 341 Query: 360 GETG 363 E+G Sbjct: 342 AESG 345 Lambda K H 0.316 0.136 0.384 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: 427 Number of extensions: 22 Number of successful extensions: 2 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: 348 Length adjustment: 30 Effective length of query: 353 Effective length of database: 318 Effective search space: 112254 Effective search space used: 112254 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: 42 (22.0 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