Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate HSERO_RS03635 HSERO_RS03635 sugar ABC transporter periplasmic protein
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__HerbieS:HSERO_RS03635 Length = 316 Score = 337 bits (865), Expect = 2e-97 Identities = 180/311 (57%), Positives = 225/311 (72%), Gaps = 9/311 (2%) Query: 13 ALSLLCTGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPD 72 A S L AAAQ A AA +PLK VGVT+G L NP+FVA+A GAE+ A KINPD Sbjct: 9 ACSTLLLAAAAQPA-------MAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPD 61 Query: 73 AKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVA 132 AKVTV+S+ YDLN Q I++FI +KVDLI++NAAD++ + PAV+KA+KAGIVVVAVDVA Sbjct: 62 AKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVA 121 Query: 133 AAGADATVQTDNTRAGELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCKMVLGKHPG 192 AAGAD TV +DNT AG +C FLA +L G+GN++I NGPPVSAV+DRV GCK K PG Sbjct: 122 AAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPG 181 Query: 193 IHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNRGGI-LI 251 I +LSD+Q+ GSR+GG+ M L PKIDAVF INDP A+GA+LA RQ R I I Sbjct: 182 IKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWI 241 Query: 252 ASVDGAPDIEAALK-ANTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLLPPTLV 310 + VDGAPD E ALK + +L AS +QDP+ +A +V IG +M+G+AP + LLP L+ Sbjct: 242 SGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKLI 301 Query: 311 TRANVNEYKGW 321 TR NV +Y+GW Sbjct: 302 TRDNVADYQGW 312 Lambda K H 0.318 0.132 0.377 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: 246 Number of extensions: 7 Number of successful extensions: 4 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: 325 Length of database: 316 Length adjustment: 28 Effective length of query: 297 Effective length of database: 288 Effective search space: 85536 Effective search space used: 85536 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 (21.7 bits) S2: 48 (23.1 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