GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Sinorhizobium meliloti 1021

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein

Query= reanno::Smeli:SMc02120
         (384 letters)



>FitnessBrowser__Smeli:SMc03865
          Length = 273

 Score =  113 bits (283), Expect = 5e-30
 Identities = 84/261 (32%), Positives = 140/261 (53%), Gaps = 30/261 (11%)

Query: 144 LLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRS 203
           + LLV    L+A++     F  T V T +  GL VT+ ++ VG  ++  LG+ +AL   S
Sbjct: 20  IALLVIAAALAAVIAANDIF--TQVFTVVLKGLGVTVFVTLVGFVLATVLGLGVALMALS 77

Query: 204 NMPVIKMLCTVFIEVIRGVPLITVLFMAS-------------VMLPL----FLPQGVTFD 246
              V++ +   + EVIRGVP++ +LF  +             V  PL    ++   V  D
Sbjct: 78  EHVVLRQIARFYTEVIRGVPILVLLFYIAFVGAPALVTVANFVAAPLISAGWIEPFVVRD 137

Query: 247 KFL--RALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKL 304
             L  RA++ + +  SA++AEV R G+Q++ KGQ E A +LGLS +Q+   +V PQA+++
Sbjct: 138 VSLMWRAIMALMIGYSAFIAEVFRAGIQSVDKGQVEAAKALGLSRYQRFRLVVFPQAIRV 197

Query: 305 VIPGIVNTFIGLFKDTSLVSIIGMFDL--LGIVRLNFSDTNWATAVTPLTGLIFAGFVFW 362
           ++P + N F+ + KD+SLVS++G+ D+  +G V  + S   + T            +V+ 
Sbjct: 198 ILPPLGNDFVAMVKDSSLVSVLGVADITQMGKVYASGSFRFFET-------YSIVAYVYL 250

Query: 363 LFCFGMSRYSGFMERLLDRSQ 383
           +   G+S     +ER L RSQ
Sbjct: 251 VLTIGLSLALRAVERRLRRSQ 271


Lambda     K      H
   0.329    0.144    0.454 

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: 245
Number of extensions: 9
Number of successful extensions: 2
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: 384
Length of database: 273
Length adjustment: 28
Effective length of query: 356
Effective length of database: 245
Effective search space:    87220
Effective search space used:    87220
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.

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