GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysL in Pseudomonas fluorescens FW300-N2C3

Align L-lysine transport protein (characterized)
to candidate AO356_05260 AO356_05260 arginine-ornithine antiporter

Query= CharProtDB::CH_019644
         (501 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05260
          Length = 475

 Score =  419 bits (1078), Expect = e-122
 Identities = 225/478 (47%), Positives = 312/478 (65%), Gaps = 16/478 (3%)

Query: 25  LIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRKPHLDS 84
           L+AL++GS +G GIFS+PQN+ + A  GA+LIGW I  VGML++AFVF  LA RKP LDS
Sbjct: 13  LVALVVGSMIGGGIFSLPQNMAARADVGAVLIGWAITAVGMLTLAFVFQTLANRKPELDS 72

Query: 85  GVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFVSALAV 144
           GVYAYA+ G GDY+GFSSAWGYW+ + +  VGY  L FSTLG++ P+F Q +  V+    
Sbjct: 73  GVYAYAKAGFGDYMGFSSAWGYWISAWMGNVGYFVLLFSTLGYFFPVFGQGNTPVAIACA 132

Query: 145 SALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLWAR-DG 203
           S L W V  +V RGI +AAF+  VTT+AK++PL+ FI++ A + F  E FT D+W   + 
Sbjct: 133 SLLLWAVHFLVLRGIKEAAFINLVTTIAKVVPLVMFIVIAA-VAFKAEVFTRDIWGEMNP 191

Query: 204 GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLVSISSL 263
            +GS+ DQVR +M+ TV+VFIGIEGASVYS +A  R+DV RATVIGF+ VL LLV ++ L
Sbjct: 192 DLGSVMDQVRHMMLVTVFVFIGIEGASVYSARAEKRADVGRATVIGFLGVLALLVLVNVL 251

Query: 264 SFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAEPLALM 323
           S G++TQ  LA L + S+A VLE +VGPWGA LISLGL +S+LGA +SW +LCAE L   
Sbjct: 252 SLGIMTQPVLAQLQNPSLAGVLEHIVGPWGALLISLGLAVSLLGALLSWALLCAEILYAT 311

Query: 324 AMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNLYLVPYL 383
           A D  +P+ +   N+  A   A  ++  +IQ+F++I   +  TY S++ LA+++ LVPYL
Sbjct: 312 ARDKTMPAFLTKENANRAPVNALWLTNGMIQLFLLITLFSAGTYTSLIYLASSMILVPYL 371

Query: 384 FSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLFYAAEP 443
           +SA Y V+L  RG+  T+  A  R              K L +G VA  Y+VWL YA   
Sbjct: 372 WSAAYAVLLCARGE--TYGQASAR------------RMKDLCIGGVALCYAVWLLYAGGV 417

Query: 444 QFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGSLSL 501
           +++L  A+   PG+I +   +  + + +F   E GV   ++  A     GL +G L+L
Sbjct: 418 KYLLLSALLYAPGVILFAQAKREQRQPLFTHVEKGVFACVMSGAGLAAYGLYSGFLAL 475


Lambda     K      H
   0.327    0.139    0.421 

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: 706
Number of extensions: 32
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: 501
Length of database: 475
Length adjustment: 34
Effective length of query: 467
Effective length of database: 441
Effective search space:   205947
Effective search space used:   205947
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 (21.7 bits)
S2: 52 (24.6 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