Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 252 bits (644), Expect = 1e-71 Identities = 158/370 (42%), Positives = 219/370 (59%), Gaps = 32/370 (8%) Query: 4 IQLTDLTKRFGDTVA-VDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYI 62 ++L L K + +V V +LSL + EFL L+GPSGCGKSTTLR++AGL+ PTSG I++ Sbjct: 6 LELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWL 65 Query: 63 GGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETL 122 G + P +RD+AMVFQ YALYPH+ VRQN+ GL+ ++AE ++R+ +VA L Sbjct: 66 GDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRT-SAAEIEQRLQQVAHNL 124 Query: 123 GIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQD 182 + LLDR+P +LSGGQ+QRVALGRA+VR P VFL+DEPLSNLDA LR ++R +++ L Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184 Query: 183 QLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL 242 Q A VYVTH+QTEA++++ RIA+++ G LQQ+ SP Y P N FVA FIG P +NL Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244 Query: 243 V-RGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDI-----EVADAAPDDAAL 296 + S ++G + P+ + R + G+RPE + EV A P L Sbjct: 245 LPLPIHSGQAWLGSR-ALPIPSHLAA----RSQVLWGLRPEHLKLATPEVERAIPVQLHL 299 Query: 297 DDH-DLQMDVTVVEPHGDQNVLHLSHP-DQPSADDALQAVTEGMHLVTRGDRVTVTIPPD 354 ++ +Q +TV + L L P DQP D + VT P+ Sbjct: 300 TENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTD-----------------LQVTFEPE 342 Query: 355 KIHLFDAETG 364 H F TG Sbjct: 343 SQHWFCPSTG 352 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: 360 Number of extensions: 16 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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