Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 171 bits (434), Expect = 2e-47 Identities = 89/240 (37%), Positives = 143/240 (59%), Gaps = 7/240 (2%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M + + L + + L+L + E L+GPSGCGK+T LR +AGL+ ++G I Sbjct: 1 MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60 Query: 61 YIGGDHMN----YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVV 116 I G ++ + P+ R I M+FQDYAL+PH+TV NI FG+ + + + + R E ++ Sbjct: 61 AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSVRLEEML 120 Query: 117 EVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 176 + + G+ R P ELSGGQQQRV++ RA+ +P++ L+DEP SN+DA++R + E Sbjct: 121 SLVKLEGLGK---RYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLE 177 Query: 177 LQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236 ++ + V+ V+VTH++ EA AD +A+ + G + Q P Y PN +VA+F+G Sbjct: 178 IRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLG 237 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: 287 Number of extensions: 12 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: 341 Length adjustment: 29 Effective length of query: 354 Effective length of database: 312 Effective search space: 110448 Effective search space used: 110448 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