Aligments for a candidate for lysL in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments 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:

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 paper from 2022 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