GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysL in Pseudomonas fluorescens GW456-L13

Align L-lysine transport protein (characterized)
to candidate PfGW456L13_1876 Arginine/ornithine antiporter ArcD

Query= CharProtDB::CH_019644
         (501 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1876
          Length = 475

 Score =  431 bits (1107), Expect = e-125
 Identities = 227/481 (47%), Positives = 315/481 (65%), Gaps = 16/481 (3%)

Query: 22  IRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRKPH 81
           +  LIAL++GS +G GIFS+PQN+ + A  GA+LIGW I  VGML++AFVF  LA RKP 
Sbjct: 10  LSALIALVVGSMIGGGIFSLPQNMAARADAGAILIGWAITAVGMLTLAFVFQTLANRKPE 69

Query: 82  LDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFVSA 141
           LDSGVYAYA+ G GDY+GFSSAWGYW+ + +  VGY  L FSTLG++VP+F + +  ++ 
Sbjct: 70  LDSGVYAYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFVPVFGEGNTPIAI 129

Query: 142 LAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLWAR 201
              S L W V  VV RGI +AAF+  VTTVAKI+PL+ FI++ A + F  + FT D+W R
Sbjct: 130 ACASVLLWTVHFVVMRGIKEAAFINQVTTVAKIVPLIMFIVIAA-VAFKADIFTADIWGR 188

Query: 202 DG-GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLVSI 260
           +    GS+ DQVR +M+ TV+VFIGIEGASVYS +A  RSDV RATVIGF+ VL LLV +
Sbjct: 189 NNPEFGSVMDQVRHMMLVTVFVFIGIEGASVYSARAEKRSDVGRATVIGFIGVLALLVLV 248

Query: 261 SSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAEPL 320
           + LS G++TQ +LA L + S+A+VLE +VGPWGA LIS+GL +S+LGA +SW +LCAE L
Sbjct: 249 NVLSLGIMTQPQLAKLQNPSLAAVLEHIVGPWGALLISVGLAISLLGALLSWALLCAEIL 308

Query: 321 ALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNLYLV 380
              A D  +P+ +   N+      A  ++  +IQ+F++I   +  TY S++ LA+++ LV
Sbjct: 309 FATAKDKTMPAFLTKENANHVPVNAMWLTNSMIQLFLLITLFSAGTYTSLIYLASSMILV 368

Query: 381 PYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLFYA 440
           PYL+SA Y V+L  RG+      A              E  K L++G +A  Y+VWL YA
Sbjct: 369 PYLWSAAYAVLLCARGETYQQAPA--------------ERIKDLLIGGIALGYAVWLLYA 414

Query: 441 AEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGSLS 500
              +++L  A+   PG+I +   R  +G+ +F   E G+   ++  A     GL +G LS
Sbjct: 415 GGLKYLLLSALLYAPGVILFAKARNEQGKPLFTVVEKGIFTCVIGGAGLAAYGLYSGLLS 474

Query: 501 L 501
           L
Sbjct: 475 L 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: 703
Number of extensions: 30
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.

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