Align TRAP-type large permease component (characterized, see rationale)
to candidate SM_b20035 SM_b20035 ABC transporter permease
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Smeli:SM_b20035 Length = 426 Score = 509 bits (1310), Expect = e-149 Identities = 247/423 (58%), Positives = 331/423 (78%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 MT+ +F+ +LLG MA+GVP+AF+L+ GV LM Y+G+F+ QI+AQN++ GAD+F L+A+P Sbjct: 1 MTISIFLGALLGPMALGVPIAFALILSGVALMLYLGLFDAQIVAQNVLNGADSFPLMAVP 60 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+LAGE+MN GGLSRRI+ A+A VGHIRGGLG VAI AA I++S+SGSA AD AAL A Sbjct: 61 FFLLAGEVMNTGGLSRRIVALAMAMVGHIRGGLGFVAIFAACILSSLSGSAVADAAALGA 120 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 +L+PMM K+G++ R++GLIA+ +I P+IPPS+ FI+FGV VSIT+LF+AGI PGL+ Sbjct: 121 LLLPMMLKSGHDPARASGLIASASIIGPIIPPSIGFILFGVVGGVSITKLFLAGIFPGLM 180 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 + AL TWL+V RK+ + PR + R+ A +LWAL +PVII+ G+K GV TPTEA Sbjct: 181 IAAALSITWLIVARKEQFELPPRQSGRLRLRAFVDSLWALFLPVIIIAGLKFGVFTPTEA 240 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 V+AAVY+LFV MV+YREL P L V + AAK +AV+MFLV A VS+WLIT A++P Sbjct: 241 GVIAAVYSLFVSMVVYRELAPAQLFHVFVSAAKISAVVMFLVACAAVSAWLITVADVPGA 300 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 + + PL+ T L+ IM+++++VGTA+D+TPTILI+TPVLMP+IKQAGIDPVYFGVL Sbjct: 301 LAALLEPLMGNQTALLIAIMVLIVIVGTAMDMTPTILIMTPVLMPVIKQAGIDPVYFGVL 360 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVIVP 420 FI+N IGL+TPPVG VLNV+ GV ++ + ++ GV PFL A+++VLFLLVLFP++V VP Sbjct: 361 FIINNSIGLITPPVGTVLNVICGVSKLSMEDLMKGVMPFLFAELIVLFLLVLFPELVTVP 420 Query: 421 ARW 423 W Sbjct: 421 VSW 423 Lambda K H 0.331 0.145 0.430 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: 550 Number of extensions: 23 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: 425 Length of database: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 51 (24.3 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