GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysL in Pseudomonas simiae WCS417

Align L-lysine transport protein (characterized)
to candidate GFF4359 PS417_22320 amino acid APC transporter

Query= CharProtDB::CH_019644
         (501 letters)



>FitnessBrowser__WCS417:GFF4359
          Length = 475

 Score =  423 bits (1088), Expect = e-123
 Identities = 224/486 (46%), Positives = 319/486 (65%), Gaps = 16/486 (3%)

Query: 17  SRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLA 76
           ++ + +  LIAL++GS +G GIFS+PQN+ + A  GA+LIGW I  VGML++AFVF  LA
Sbjct: 5   AQKLRLSALIALVVGSMIGGGIFSLPQNMAARAEVGAVLIGWAITAVGMLTLAFVFQTLA 64

Query: 77  RRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDH 136
            RKP LDSGVYAYA+ G GDY+GFSSAWGYW+ + +  VGY  L FSTLG++ P+F Q +
Sbjct: 65  NRKPELDSGVYAYAKAGFGDYMGFSSAWGYWISAWMGNVGYFVLLFSTLGYFFPIFGQGN 124

Query: 137 PFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTV 196
             V+    S L W V  +V RGI +AAF+  +TTVAKI+PLL FI+ +A + F  E FT 
Sbjct: 125 TPVAIGCASLLLWAVHFLVLRGIKEAAFINQITTVAKIVPLLMFIV-IAGVAFKAEIFTR 183

Query: 197 DLW-ARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLL 255
           D+W   +  +G++ DQVR +M+ TV+VFIGIEGASVYS +A  RSDV RATVIGF+ VL 
Sbjct: 184 DIWGVGNPNMGNVVDQVRNMMLVTVFVFIGIEGASVYSARAEKRSDVGRATVIGFLGVLA 243

Query: 256 LLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQML 315
           LLV ++ LS G+++Q +LA L + S+A VLE +VGPWGA  IS+GL +S+LGA +SW +L
Sbjct: 244 LLVLVNVLSLGIMSQPQLAQLQNPSLAGVLEHIVGPWGAMAISIGLAVSLLGALLSWALL 303

Query: 316 CAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLAT 375
           CAE L   A D  +P+ +   N+      A  ++ ++IQ+F++I   + +TY +++ LA+
Sbjct: 304 CAEILYATAHDKTMPAFLKKENANQVPVNALWLTNVMIQVFLVITLFSHSTYTTLIYLAS 363

Query: 376 NLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSV 435
           ++ LVPYL+SA Y V+L+ RG+     H G R  D             L+VGL+A  Y+V
Sbjct: 364 SMILVPYLWSAAYAVLLSGRGETYQGAH-GQRIKD-------------LLVGLIALGYAV 409

Query: 436 WLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLV 495
           WL YA   +++L  A+   PG+I +   +  + + +F   E G+   ++  A     GL 
Sbjct: 410 WLLYAGGLKYLLLSALLYAPGVILFALAKREQDQPLFTHVEKGIFSCVIAGAGLAAYGLY 469

Query: 496 NGSLSL 501
           +G LSL
Sbjct: 470 SGVLSL 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: 708
Number of extensions: 33
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.

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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