GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysL in Pseudomonas fluorescens FW300-N2E3

Align L-lysine transport protein (characterized)
to candidate AO353_20050 AO353_20050 arginine-ornithine antiporter

Query= CharProtDB::CH_019644
         (501 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20050
          Length = 497

 Score =  389 bits (999), Expect = e-112
 Identities = 210/484 (43%), Positives = 309/484 (63%), Gaps = 16/484 (3%)

Query: 18  RTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLAR 77
           R +S+  LIAL++GS +G+GIFS+PQN+ + AG GA+LIGWLI GVGMLS+A V+  L+ 
Sbjct: 30  RRLSLSLLIALVVGSMIGSGIFSLPQNMAAGAGAGAILIGWLITGVGMLSLALVYQTLSN 89

Query: 78  RKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHP 137
           R+P LD+GV+AYAR   G+++GF+SAWGYW+ + I  V Y  + F+ L ++ PLF + + 
Sbjct: 90  RQPELDNGVFAYARALGGEFLGFNSAWGYWISAWIGNVSYLVILFAALSYFFPLFGEGNN 149

Query: 138 FVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVD 197
             +  A S + W +  ++ RG+  AA    +TT+AKI+PLL FI LV    F  E F VD
Sbjct: 150 KAAIAAASLVLWSLHWMILRGMRTAARANALTTLAKIVPLLLFIGLV-IAAFQRETFMVD 208

Query: 198 LWARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLL 257
            W     +GS  DQV+  M+ TVWVFIGIEGA+V+S +A  R +V RATVIGFV  LLLL
Sbjct: 209 FWGAPA-LGSTLDQVKSTMLVTVWVFIGIEGANVFSARAAERVNVGRATVIGFVLTLLLL 267

Query: 258 VSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCA 317
           +++S LS G+L Q ELAAL + SM+ VLEAV GPWGA LIS+GL +SV GA ++W +L A
Sbjct: 268 IAVSLLSLGILRQPELAALKNPSMSGVLEAVAGPWGAMLISVGLIISVGGALLAWTLLAA 327

Query: 318 EPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNL 377
           E +   A + ++P  +   N+ GA   A  I+   IQ+F+++   +  +Y++++ LAT++
Sbjct: 328 ESVFTPAKEKVMPGPLALENTHGAPANALWITNGCIQLFLLLTLYSSASYLALISLATSM 387

Query: 378 YLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWL 437
            L+PYLFS  Y + L  +G      +AG           +    + + +  VAT+Y +WL
Sbjct: 388 ILLPYLFSGLYALKLTWQGA----TYAG----------HKALQLRDMAIASVATLYCLWL 433

Query: 438 FYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNG 497
            +AA P+++L  A+   PG + Y+ T+  R  Q  N FE G+++V+  AA+     L +G
Sbjct: 434 LFAAGPKYMLLSALLYAPGSLIYLATKRARQGQALNGFEWGLLIVIWAAAAFAGWMLWSG 493

Query: 498 SLSL 501
            L+L
Sbjct: 494 KLAL 497


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: 719
Number of extensions: 39
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: 497
Length adjustment: 34
Effective length of query: 467
Effective length of database: 463
Effective search space:   216221
Effective search space used:   216221
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