Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate SM_b20352 SM_b20352 sugar ABC transporter permease
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__Smeli:SM_b20352 Length = 354 Score = 188 bits (478), Expect = 1e-52 Identities = 101/319 (31%), Positives = 177/319 (55%), Gaps = 20/319 (6%) Query: 21 LDDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSV 80 L ++ L A + F ++ NFLS N+ + ++ A M + + +G DLSV Sbjct: 25 LRTFIALFAVVAFF---SIFAPNFLSTANLILMSKHVALNAFLAMGMTFVIITGGIDLSV 81 Query: 81 GSVIACAGVVAAVVMRDTNSVFLGISA----------ALVMGLIVGLINGIVIAKLRVNA 130 GS++ G+VA ++ + + G + L +G+++G +NG++I KL V Sbjct: 82 GSIVGLCGMVAGGLILNGIDLQFGYTVYFNVVEVCLITLAVGIVIGAVNGLLITKLNVAP 141 Query: 131 LITTLATMQIVRGLAYIFANGKA----VG---VSQESFFVFGNGQMFGVPVPILITIVCF 183 I TL T+ + RG A + + G+ VG ++ F G+G++ G+PV I + IV Sbjct: 142 FIATLGTLYVARGFALLSSGGQTFPNLVGKPELATTGFAFLGSGRLLGLPVSIWVLIVVA 201 Query: 184 LFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMT 243 L ++ YT GR+ A+GGN+ AA ++G+ VDR K+ ++ G A+ G++++S + Sbjct: 202 LAAAYVARYTPIGRHIFAVGGNERAARMSGIRVDRVKMFVYMFSGFCAAIVGLVISSELM 261 Query: 244 SGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQY 303 + P G FEL I+A VLGG S+SGG G I I G ++ I+ + + + I +F+Q Sbjct: 262 ASHPATGNSFELNAIAAAVLGGTSMSGGRGTIGGTIIGAFVIGILSDGLVMMGISSFWQM 321 Query: 304 VIRGSILLLAVVIDRLKQR 322 VI+G ++++AVV+D+ ++R Sbjct: 322 VIKGIVIIVAVVVDQAQRR 340 Lambda K H 0.330 0.144 0.420 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: 276 Number of extensions: 14 Number of successful extensions: 1 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: 322 Length of database: 354 Length adjustment: 28 Effective length of query: 294 Effective length of database: 326 Effective search space: 95844 Effective search space used: 95844 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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