Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate SM_b20659 SM_b20659 sugar uptake ABC transporter permease
Query= TCDB::Q9KZ07 (334 letters) >FitnessBrowser__Smeli:SM_b20659 Length = 310 Score = 153 bits (386), Expect = 6e-42 Identities = 105/304 (34%), Positives = 158/304 (51%), Gaps = 40/304 (13%) Query: 37 YAMIAPVAVVIGVLVLYPLGYGLYLTLTDANSLNSARTIGVNEIEATYKFVGLDNYADIL 96 + + P AV + + YPLG G++L TD IG + + F+G++NY + Sbjct: 25 FLFMLPAAVFLICFLTYPLGLGVWLGFTDTR-------IGRDGV-----FIGIENYEFLA 72 Query: 97 WGPTAYDRFWSHFIWTIVWTAVCVGLHFFIGLGLALLLNQKLRGRTFYRLILVLPWAVPT 156 FW T+++T V L F +GL LALLLN+ L ++F+R I++LPW VPT Sbjct: 73 RDSV----FWLSVYNTLLYTFVASILKFVLGLWLALLLNENLPFKSFFRAIVLLPWVVPT 128 Query: 157 FVTV--FGWRF---------MLADQGIINSALDWLHLPTPAWLEDTFWQRFSAIMVNTWC 205 ++ F W + L GII+ +++L P A R S I N W Sbjct: 129 VLSALAFWWIYDSQFSIISWSLMQLGIIDGPINFLGDPNNA--------RASVIAANVWR 180 Query: 206 GVPFMMVSLLGGLQSIDNSLYEASEMDGANAWQRFRYVTLPGLRSVSSTVVLLGIIWTFN 265 G+PF+ +SLL GLQ+I SL EA+ +DGA +WQRFRYVTLP L + + V+ +++TF Sbjct: 181 GIPFVAISLLAGLQTIPASLQEAASLDGATSWQRFRYVTLPMLTPIIAVVMTFSVLFTFT 240 Query: 266 QFAVIFLLF-GNTAPDAQILVTWAYQLGF-GQQPRDFAQSAAYGILLLAILIVFTSF--- 320 F +I++L G ++ T ++Q G G Q + A A I L I+F+ F Sbjct: 241 DFQLIYVLTKGGPVNATHLMATLSFQRGIPGGQLGEGAAIAVAMIPFLLAAIMFSFFGLQ 300 Query: 321 YRRW 324 R+W Sbjct: 301 RRKW 304 Lambda K H 0.328 0.142 0.468 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: 297 Number of extensions: 13 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: 310 Length adjustment: 28 Effective length of query: 306 Effective length of database: 282 Effective search space: 86292 Effective search space used: 86292 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 (21.7 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