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_05265 AO356_05265 arginine-ornithine antiporter

Query= CharProtDB::CH_019644
         (501 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05265
          Length = 475

 Score =  426 bits (1094), Expect = e-123
 Identities = 219/487 (44%), Positives = 314/487 (64%), Gaps = 16/487 (3%)

Query: 16  TSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVL 75
           T   + +  L+AL++GS +G GIFS+PQN+ + A  GA+LIGW I  VGML++AFVF  L
Sbjct: 4   TPGKLRLGALVALVVGSMIGGGIFSLPQNMAASADVGAVLIGWAITAVGMLTLAFVFQTL 63

Query: 76  ARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQD 135
           A RKP LD GVY YA+ G GDY+GFSSAWGYW+ + +  VGY  L FSTLG++ P+F + 
Sbjct: 64  ANRKPDLDGGVYVYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFFPIFGEG 123

Query: 136 HPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFT 195
           +   + +  S L W V  +V RGI +AAF+  VTT+AK++PLL F +L+A   F  + FT
Sbjct: 124 NTVAAVIGASVLLWAVHFLVLRGIKEAAFINLVTTIAKVVPLLLF-VLIAVFAFRLDIFT 182

Query: 196 VDLW-ARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVL 254
            D+W  ++  +GS+ +QVR +M+ TVWVFIGIEGAS++S +A  RSDV +ATVIGF+ VL
Sbjct: 183 ADIWGVKNPDLGSVMNQVRKMMLVTVWVFIGIEGASIFSARAEKRSDVGKATVIGFITVL 242

Query: 255 LLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQM 314
           L LV ++ LS G++TQ ELA L + SMA+VLE VVG WGA LIS+GL +S+LGA +SW +
Sbjct: 243 LFLVLVNVLSLGIMTQPELAKLQNPSMAAVLEHVVGHWGAVLISVGLIISLLGALLSWVL 302

Query: 315 LCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLA 374
           LCAE +   A D  +P  +   N+      A  ++  ++Q+F++I   + +TY+S++ LA
Sbjct: 303 LCAEIMFAAAKDHTMPEFLRRENANHVPANALWLTNAMVQLFLVITLFSASTYLSLIYLA 362

Query: 375 TNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYS 434
           T++ LVPYL+SA Y V+LA RG+                E    E RK L++G +A +Y+
Sbjct: 363 TSMILVPYLWSAAYAVLLAVRGETY--------------EGFAAERRKDLLIGAIALIYA 408

Query: 435 VWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGL 494
           VWL YA   +++L  A+   PG I +   +   G+ VF   E  +   ++  A     GL
Sbjct: 409 VWLLYAGGIKYLLLSALLYAPGAILFAKAKHELGKPVFTSVEKLIFAAVIAGALVAAYGL 468

Query: 495 VNGSLSL 501
            +G L+L
Sbjct: 469 YDGFLTL 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: 732
Number of extensions: 36
Number of successful extensions: 6
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:

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