GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Sinorhizobium meliloti 1021

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate SMa2309 SMa2309 ABC transporter permease

Query= reanno::WCS417:GFF4322
         (281 letters)



>FitnessBrowser__Smeli:SMa2309
          Length = 273

 Score =  181 bits (460), Expect = 1e-50
 Identities = 99/270 (36%), Positives = 157/270 (58%), Gaps = 7/270 (2%)

Query: 17  IYAVLILAVLL-YLVPLVVMLLTSFKTPEDISSGNLLSWPT---VVTGIGWVKAWATVDG 72
           +Y  ++ A+L+ +L PL  ++LTSF++  D+ SGNL  WPT   VV     V     + G
Sbjct: 6   LYMTVVGAILIIWLAPLFAVILTSFRSMADVMSGNLWGWPTEIAVVENYTAVFTQTPMAG 65

Query: 73  YFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPASFT 132
           YF NS+ IT+P+V+   ++  L G+VL+ +RF G+ + F L + G FLP Q +++P    
Sbjct: 66  YFLNSLVITIPSVIGVLSLSTLAGFVLARYRFPGNMVIFALFVGGNFLPHQIMMIPVRDL 125

Query: 133 LGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQIIL 192
           + ++ L  TTT L+  HV +   F TLF RN+  ++PD L +AAR +GA  F     +++
Sbjct: 126 MVRLNLYDTTTALIIFHVAFQTGFATLFMRNFIAALPDELFQAARAEGATPFQTLIHVVV 185

Query: 193 PMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDS-QPITVALNNLVNTSTGAKEYNVDMAA 251
           P+  P      I  FT IWND+ + VV +  D+ +P+T  L NL      A  +N+  A 
Sbjct: 186 PLVRPAWAALAILLFTFIWNDYFWAVVLTVSDNVKPVTAGLANLRGEWVSA--WNLISAG 243

Query: 252 AMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281
            +I  +P ++++ +  K+F+ GLT GAVKG
Sbjct: 244 TIIVAVPPVVMFFLMQKHFIAGLTMGAVKG 273


Lambda     K      H
   0.328    0.141    0.435 

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: 228
Number of extensions: 20
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: 281
Length of database: 273
Length adjustment: 25
Effective length of query: 256
Effective length of database: 248
Effective search space:    63488
Effective search space used:    63488
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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