Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 229 bits (583), Expect = 2e-64 Identities = 122/284 (42%), Positives = 183/284 (64%), Gaps = 7/284 (2%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 I+++ ++K FGD A+DD++L++ EF+ ++GPSGCGK+T LR++AG +T + G+I I Sbjct: 10 IEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRIS 69 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA-ETL 122 G + P R + VFQ YAL+PH+ V NI FGL+ ++ T + + V+ A + + Sbjct: 70 GKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKK--TPKQTIGKKVKAALKMV 127 Query: 123 GIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQD 182 G+ D R D LSGGQQQRVA+ RAIV +PEV L+DEPL+ LD K+R +M+ EL+ + Sbjct: 128 GMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHK 187 Query: 183 QLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL 242 L +T VYVTH+Q EA+T++D I VM +G++QQ+ +P + Y+EP N FVA+FIGE N+ Sbjct: 188 SLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGES--NI 245 Query: 243 VRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEV 286 + GT V F E V E + + +RPED+ + Sbjct: 246 LNGTMIHDKLV--RFCGTEFECVDEGFGENTPVDVVIRPEDLYI 287 Score = 25.8 bits (55), Expect = 0.003 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 344 GDRVTVTIPPDKIHL 358 GDRV +TIPPD I + Sbjct: 444 GDRVGITIPPDAIRV 458 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: 459 Number of extensions: 24 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 463 Length adjustment: 32 Effective length of query: 351 Effective length of database: 431 Effective search space: 151281 Effective search space used: 151281 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 Apr 09 2024. 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