Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 275 bits (704), Expect = 1e-78 Identities = 172/373 (46%), Positives = 229/373 (61%), Gaps = 27/373 (7%) Query: 1 MGQIQLTDLTKRFGDT-VAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M +++L L K + + V V + S +I D E LVLVGPSGCGK+T LRM+AGLE+ + G Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 + IG +N P++RDIAMVFQ+YALYPHMTV +N+ FGL+ G AE + RV E A Sbjct: 61 LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLR-GQPKAEIERRVAEAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L + LD +P LSGGQ+QRVALGRA+VRDP+VFL+DEPLSNLDAKLR MR E+ Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 + +L T VYVTH+Q EAMT+ RI V++ G +QQ+ +P Y P NLFVA F+G P Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239 Query: 240 INLVRGTRSESTFVGEHFSYPLDEDV---------MESVDDRDDFVLGVRPEDIEV-ADA 289 +NL+RG G + P E V +E+ DR D V+G+RPED+ + ADA Sbjct: 240 MNLLRGILYRDG--GWKLAMPQGELVLGELPQGAALEAWRDR-DIVVGLRPEDLLLCADA 296 Query: 290 APDDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTV 349 A AA L + VVEP G++ L+L H + AL + L G + Sbjct: 297 A--GAA-----LAAQLEVVEPVGNEVFLNLRH-----GELALVSRMPPRELPAPGSTLHF 344 Query: 350 TIPPDKIHLFDAE 362 P+++H FDA+ Sbjct: 345 GFAPERLHFFDAK 357 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: 331 Number of extensions: 10 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: 364 Length adjustment: 30 Effective length of query: 353 Effective length of database: 334 Effective search space: 117902 Effective search space used: 117902 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