Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate SMa1341 SMa1341 ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__Smeli:SMa1341 Length = 319 Score = 173 bits (438), Expect = 5e-48 Identities = 90/249 (36%), Positives = 148/249 (59%), Gaps = 9/249 (3%) Query: 43 PTVEIMAKPPVWIPETLSLDA-YRAMFSGAGQ---GGVPVWDYFRNSLIVSVTSTVIALA 98 P E A P W E L D + + SG GQ G P + F NSLIV++TSTV+A+A Sbjct: 75 PEPEDYAAAPWW--ERLVFDGGEKVVRSGRGQVQLSGYP--NRFMNSLIVAITSTVLAVA 130 Query: 99 IGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGIIDTHFSLILTYV 158 +G Y F+R++ K ++ + + TR +P + +++P+F++Y G+ DTH+ LI+ Y Sbjct: 131 MGTFTAYGFSRFKVKGEADLLFFILSTRMLPPVVVAIPMFLMYRAVGLNDTHWGLIILYT 190 Query: 159 ALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPGIASAGIFAFLTS 218 A N+ F++WL+ GF ++PK+ EAA +DG T +AF+++ P A GIA+ +F F+T+ Sbjct: 191 AFNLSFSVWLMKGFIDEIPKEYEEAALVDGYTRLEAFFKIVLPEAATGIAATAVFCFITA 250 Query: 219 WNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVMIVPALTLTFIIQKHLV 278 WNEYA A +T ++T P + DW + A + ++P TF+++ HL+ Sbjct: 251 WNEYAFALIMTNR-RAQTAPPFIPSQVGSGLPDWTVIAAGTFLFLLPVAIFTFLLRNHLL 309 Query: 279 SGLTFGAVK 287 G++FGA++ Sbjct: 310 RGMSFGAIR 318 Lambda K H 0.328 0.141 0.442 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: 278 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 288 Length of database: 319 Length adjustment: 27 Effective length of query: 261 Effective length of database: 292 Effective search space: 76212 Effective search space used: 76212 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: 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