GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AGP1 in Klebsiella michiganensis M5al

Align general amino acid permease AGP1 (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter

Query= CharProtDB::CH_091105
         (633 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19685 BWI76_RS19685 lysine
           transporter
          Length = 489

 Score =  262 bits (669), Expect = 3e-74
 Identities = 140/470 (29%), Positives = 244/470 (51%), Gaps = 10/470 (2%)

Query: 112 KSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQA 171
           ++  L++ ++ RH+ MIA+G  IGTGL V +G  +  AGP G L+ Y ++G ++Y ++ +
Sbjct: 9   EAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTS 68

Query: 172 CGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTS 231
            GE+A  +  ++G +  Y    V++GFGFA+ W Y   W     ++LV A + + YW   
Sbjct: 69  LGELA-AFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPD 127

Query: 232 VNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGF 291
               V+  +F  ++  +N    +G+ EAE++F+  K+  +  F I+G+++  G       
Sbjct: 128 APGWVWSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGIFKGAQP 187

Query: 292 IGGKYWH-DPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAA 350
            G   W  D   F G      F  +    +   F+F G+E I I   E  NP K IP A 
Sbjct: 188 AGWSNWVIDDAPFAGG-----FAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAV 242

Query: 351 KQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFINA 410
           +Q+ +RIL  ++  I+++  ++PY    LL +       SP+ +     G+      +NA
Sbjct: 243 RQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNA 302

Query: 411 VILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAFCA 470
           VIL +VLS  NS  Y+S R+  TL+  G AP++FS + + G P  A+  + + A + F +
Sbjct: 303 VILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLS 362

Query: 471 ASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVWGSA 530
           +    + V+ WLL  SG++    W  I +SH RFRR   +QG  L +L ++S     G  
Sbjct: 363 SMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGNDLNDLPYRSGFFPLGPI 422

Query: 531 YACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIALYVGYKV 580
           +A ++ ++I + Q + A     +  +D       Y+ +P+ + ++ GYK+
Sbjct: 423 FAFVLCLIITLGQNYEAFL---KDTIDWGGVAATYIGIPLFLVIWFGYKL 469


Lambda     K      H
   0.324    0.138    0.424 

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: 28
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: 633
Length of database: 489
Length adjustment: 36
Effective length of query: 597
Effective length of database: 453
Effective search space:   270441
Effective search space used:   270441
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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