GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Sinorhizobium meliloti 1021

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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