Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SMc03062 SMc03062 alpha-glucoside ABC transporter permease
Query= uniprot:A8LLL5 (334 letters) >FitnessBrowser__Smeli:SMc03062 Length = 336 Score = 408 bits (1048), Expect = e-118 Identities = 206/336 (61%), Positives = 259/336 (77%), Gaps = 8/336 (2%) Query: 1 MHPAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGP---KAGRNINRANQIRPWIFL 57 M ++T++ GV C YF+ N LD + +P+KG A RN+ AN IRPW+FL Sbjct: 1 MEQLIAAILTMVAGVLVCAAYFWSTNLVLDWI-FPSKGKFGAVASRNLRIANSIRPWLFL 59 Query: 58 FPALFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWL 117 PAL L LYL YPVV+++ LSL R GG +VGL NY+ M ++ +F +++ NN WL Sbjct: 60 APALLALTLYLVYPVVQSVWLSLHGR---GGQNFVGLSNYSWMINDGEFRQSIFNNFLWL 116 Query: 118 IVVPALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQI 177 +VVPALST FGL+ A LTDRI WGN+AK++IFMPMAISFVGA+VIWK +YD R EQI Sbjct: 117 LVVPALSTFFGLIIAALTDRIWWGNIAKTLIFMPMAISFVGAAVIWKFIYDYRAAGSEQI 176 Query: 178 GILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAI 237 G+LNAI+V LGG+P ++T+PFWNNFFLM++L+W+QTGFAMVILSAALRGIPEETIEAA+ Sbjct: 177 GLLNAIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVILSAALRGIPEETIEAAV 236 Query: 238 IDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDK 297 IDGA+ QIFFKI VPQI T+ VVWTTIT++VLKVFDIV AMTNGQW++QVLAN MFD Sbjct: 237 IDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNGQWQSQVLANLMFDW 296 Query: 298 LFR-ANDWGVGSASAMVIMLLVTPILIWNIHSARKE 332 +FR D+G G+A A+VIM+LV PI+IWNI +A +E Sbjct: 297 MFRGGGDFGRGAAIAVVIMILVVPIMIWNIRNATRE 332 Lambda K H 0.329 0.143 0.455 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: 443 Number of extensions: 16 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: 334 Length of database: 336 Length adjustment: 28 Effective length of query: 306 Effective length of database: 308 Effective search space: 94248 Effective search space used: 94248 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