GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupC in Klebsiella michiganensis M5al

Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS19710 BWI76_RS19710 NupC/NupG family nucleoside CNT transporter

Query= uniprot:A0KU05
         (419 letters)



>FitnessBrowser__Koxy:BWI76_RS19710
          Length = 416

 Score =  414 bits (1063), Expect = e-120
 Identities = 211/426 (49%), Positives = 297/426 (69%), Gaps = 18/426 (4%)

Query: 1   MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60
           M+I+ SL+G+VVLLAI F LS NKK I++RTVG AL +Q   GG +LY P GK +++  +
Sbjct: 1   MDIMRSLLGMVVLLAIAFALSVNKKRISIRTVGAALLLQIVIGGVMLYFPPGKWLVEQAA 60

Query: 61  DAVSSVIGYAQNGIGFLFGDLANFKL-------GFIFAVNVLPVIVFFSSLIAVLYYLGI 113
             V  V+ Y+  G  F+FG L   K+       GFIFA  VLP I+F ++LI++LYYLG+
Sbjct: 61  LGVHKVMSYSDAGSAFIFGSLVGPKMDVLFDGAGFIFAFRVLPAIIFVTALISLLYYLGV 120

Query: 114 MQWIIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGG 173
           M  +IRI+GG  QKAL  S+ ES  A   IF+GQ E P +V+PFI  + ++ELF  +  G
Sbjct: 121 MGLLIRILGGIFQKALNISKIESFVAVTTIFLGQNEIPAIVKPFINKLNRNELFTAICSG 180

Query: 174 LASIAGSVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDK 233
           +ASIAGS++ GYA MGVPI+YL+AAS MA PGG+L A+++ P TE ++   D L      
Sbjct: 181 MASIAGSMMIGYAGMGVPIDYLLAASLMAIPGGILFARMLSPATEASQVTFDNLSFSETP 240

Query: 234 PANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGY 293
           P +V++AAA+GA +G+ +A  V  +++AFV +IA++NGIIGG+GGWFG    TLE I G+
Sbjct: 241 PKSVIEAAASGAMTGLKIAAGVATVVMAFVAIIALLNGIIGGIGGWFGFGHATLEGIFGF 300

Query: 294 IFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLAMT 353
           +  PLA+++GV W++A +AGS IGQK+ +NEFVAYLNF+PYL+           +G  + 
Sbjct: 301 LLAPLAWIMGVDWSDATLAGSLIGQKLAINEFVAYLNFSPYLQ-----------SGGNLD 349

Query: 354 DRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATIA 413
            +T AIISFALCGFAN  SI +++G   A++P R  ++A+LG+RA+ A +L+NLMSATIA
Sbjct: 350 VKTVAIISFALCGFANFGSIGVVVGAFSAISPQRAPEIAQLGLRALAAATLSNLMSATIA 409

Query: 414 GLFLAI 419
           G F+ +
Sbjct: 410 GFFIGL 415


Lambda     K      H
   0.325    0.142    0.407 

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: 591
Number of extensions: 34
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: 419
Length of database: 416
Length adjustment: 32
Effective length of query: 387
Effective length of database: 384
Effective search space:   148608
Effective search space used:   148608
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: 40 (21.6 bits)
S2: 50 (23.9 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