Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 281 bits (720), Expect = 2e-80 Identities = 157/317 (49%), Positives = 209/317 (65%), Gaps = 15/317 (4%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 + + +L K +G T + D+++ I+ +FLVLVGPSGCGKST L +AGLE T G I IG Sbjct: 5 LDIKNLYKSYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIG 64 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 G M + P++RDIAMVFQ YALYP MTV +NI FG++ G A +D ++ +VA+ L Sbjct: 65 GKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVR-GVDQATQDRKLAQVAQQLQ 123 Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183 I LL+R+P +LSGGQ+QRVA+GRA+VRDP++FL DEPLSNLDAKLR EMRTE+++L Sbjct: 124 IEPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHN 183 Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243 L + VYVTH+Q EAMT+A +I VM G +QQ+ SP E Y+ P NLFVA+F+G P +NL+ Sbjct: 184 LGASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLI 243 Query: 244 --------RGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA 295 GTR E T P+ ++ D +D +LGVRPEDI D +AA Sbjct: 244 PAKAHRADEGTRIEIT---RKSGEPIVLTDTKNRDLPEDVILGVRPEDIADPDLRGAEAA 300 Query: 296 LDDHDLQMDVTVVEPHG 312 L + +VEP G Sbjct: 301 QAAECL---IDMVEPAG 314 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: 343 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: 365 Length adjustment: 30 Effective length of query: 353 Effective length of database: 335 Effective search space: 118255 Effective search space used: 118255 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 24 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