Aligments for a candidate for lysL in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for lysL in Pseudomonas putida KT2440

Align L-lysine transport protein (characterized)
to candidate PP_1003 PP_1003 arginine/ornithine antiporter

Query= CharProtDB::CH_019644
         (501 letters)



>lcl|FitnessBrowser__Putida:PP_1003 PP_1003 arginine/ornithine
           antiporter
          Length = 475

 Score =  419 bits (1076), Expect = e-121
 Identities = 227/478 (47%), Positives = 315/478 (65%), Gaps = 16/478 (3%)

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

Query: 85  GVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFVSALAV 144
           GVYAYA+ G G+Y+GFSSAWGYW+ + +  VGY  L FSTLG Y P+F + +  ++    
Sbjct: 73  GVYAYAKAGFGEYMGFSSAWGYWISAWLGNVGYFVLLFSTLGFYFPVFGEGNTPIAIGCA 132

Query: 145 SALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLWA-RDG 203
           S L W V  +V RGI +AAF+  VTTVAK++PLL F+++ AF  F  + FT D+W   + 
Sbjct: 133 SLLLWSVHFLVLRGIKEAAFINQVTTVAKVVPLLIFVVIAAF-AFRADIFTRDIWGLSNP 191

Query: 204 GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLVSISSL 263
             GS+ +QVR +M+ TV+VFIGIEGASVYS +A+ RSDV +ATVIGF+ VL LLV ++ L
Sbjct: 192 QFGSVLEQVRNMMLVTVFVFIGIEGASVYSGRAQRRSDVGKATVIGFLGVLALLVLVNVL 251

Query: 264 SFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAEPLALM 323
           S G++TQ ELA L + S+ASVLE +VGPWGA LISLGL +S+LGA +SW +LCAE L   
Sbjct: 252 SLGIMTQPELAGLQNPSLASVLEHIVGPWGALLISLGLAVSLLGALLSWALLCAEILYAT 311

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

Query: 384 FSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLFYAAEP 443
           +SA Y V+LA R +     +AG            R  RK L+V LVA +Y+VWL YA   
Sbjct: 372 WSAAYAVLLAMRAE----TYAG----------QPRLRRKDLLVALVALLYAVWLLYAGGL 417

Query: 444 QFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGSLSL 501
           +++L  A+   PG+I +   +  +G+ +F  +E  +   ++V A+     L +G LSL
Sbjct: 418 KYLLLSALLYAPGVILFARAKHEQGQTLFTAWEKLIFAAVLVGAALAAYALYSGLLSL 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: 710
Number of extensions: 35
Number of successful extensions: 4
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.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources