Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 280 bits (716), Expect = 4e-80 Identities = 164/371 (44%), Positives = 215/371 (57%), Gaps = 22/371 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +Q+ + K FG T + + +DI D +F VLVGPSGCGKST LRM+AGLE T+G+I Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 IG +N P+ RDIAMVFQ+YALYPHMTV N+ F L+ +G E +V + + Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKG-DKEEIKRKVAKASA 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 LG+ LL+R P +LSGGQ+QRVA+GRAIVRDP+VFL DEPLSNLDAKLR +MR E++ L Sbjct: 120 ILGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKEL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L T+VYVTH+Q EAMTMAD+I VM DG ++Q P Y P+NLFVA FIG P + Sbjct: 180 HQRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAM 239 Query: 241 NLVRGTRSESTF-------VGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDD 293 N V G S G P D D + + GVRPE + + Sbjct: 240 NFVPGVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQ-RVIYGVRPEHLTL------- 291 Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPP 353 + LQ V+VVEP G ++ + ++ H GD + + Sbjct: 292 -GMPGQGLQTRVSVVEPTGANTEIY-----SRFCEAEFISIFRERHDFAAGDILNLVPDH 345 Query: 354 DKIHLFDAETG 364 HLFDA++G Sbjct: 346 QHTHLFDADSG 356 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: 358 Number of extensions: 19 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: 359 Length adjustment: 30 Effective length of query: 353 Effective length of database: 329 Effective search space: 116137 Effective search space used: 116137 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: 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