GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC in Shewanella oneidensis MR-1

Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate 199290 SO0093 NupC family protein (NCBI ptt file)

Query= uniprot:A0KU05
         (419 letters)



>lcl|FitnessBrowser__MR1:199290 SO0093 NupC family protein (NCBI ptt
           file)
          Length = 406

 Score =  435 bits (1119), Expect = e-126
 Identities = 212/419 (50%), Positives = 308/419 (73%), Gaps = 14/419 (3%)

Query: 1   MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60
           M+ +MS +G+ VL+ IG+L S NK+ I  +T+ GALA+Q   G FV++VP G  I++++S
Sbjct: 1   MSTIMSCIGIAVLVFIGYLFSENKRQIKFKTIAGALALQILLGAFVMFVPAGVTIIEAMS 60

Query: 61  DAVSSVIGYAQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIRI 120
             V+SVI ++ +G+ F+FGDLAN+KLGF+F +NVL V++F S+LI+VLYYL +MQ+II I
Sbjct: 61  SGVNSVIAFSNSGLTFVFGDLANYKLGFVFVINVLCVVIFISALISVLYYLKVMQFIINI 120

Query: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS 180
           IGGGL K LGTS+ ES+SATANIFVG  EAP +VRP +  MT+SELFA+M GGLAS+AG 
Sbjct: 121 IGGGLSKVLGTSKAESLSATANIFVGPIEAPSMVRPLVKNMTRSELFAVMTGGLASVAGG 180

Query: 181 VLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPANVLDA 240
            + GY  +G+  +Y++ A FM AP GLL AKL+ P+TE    + D   ED D+P  +L+A
Sbjct: 181 TMVGYINLGIDPKYILTACFMTAPAGLLFAKLLCPQTEHNLVNNDNKIEDADQPKGLLEA 240

Query: 241 AAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAF 300
              G+  GM+  + V A+L++FV +IA++NGIIG +G  F ++ LTLE+I+GY+  PLAF
Sbjct: 241 ITDGSLMGMNQVITVTALLVSFVAIIALLNGIIGSIGNLFSIDKLTLEMIIGYLLSPLAF 300

Query: 301 LIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLAMTDRTKAII 360
           L+GVPW+EA+ A S IGQKI +NEFVAY++F           + V++T   ++D+T+AI+
Sbjct: 301 LMGVPWSEAIPAASIIGQKIAINEFVAYISF-----------LEVSNT---LSDKTQAIV 346

Query: 361 SFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATIAGLFLAI 419
            F+LCGFAN+ S+A+++GG+ AM P++R  + ++G R ++A  LANLMS TIAG  +++
Sbjct: 347 VFSLCGFANIGSLAMVVGGIAAMCPDKRELITQIGPRVLLAAILANLMSGTIAGALVSL 405


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: 529
Number of extensions: 23
Number of successful extensions: 2
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: 406
Length adjustment: 31
Effective length of query: 388
Effective length of database: 375
Effective search space:   145500
Effective search space used:   145500
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 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, 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