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 200392 SO1214 NupC family protein (NCBI ptt file)

Query= uniprot:A0KU05
         (419 letters)



>lcl|FitnessBrowser__MR1:200392 SO1214 NupC family protein (NCBI ptt
           file)
          Length = 432

 Score =  754 bits (1947), Expect = 0.0
 Identities = 394/432 (91%), Positives = 408/432 (94%), Gaps = 13/432 (3%)

Query: 1   MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60
           MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILK +S
Sbjct: 1   MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKGMS 60

Query: 61  DAVSSVIGYAQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIRI 120
           DAVSSVIG+AQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLG+MQWIIRI
Sbjct: 61  DAVSSVIGFAQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLGVMQWIIRI 120

Query: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS 180
           IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFA+MVGGLASIAGS
Sbjct: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAVMVGGLASIAGS 180

Query: 181 VLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPANVLDA 240
           VLAGYAQMGVPIE+LVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPANVLDA
Sbjct: 181 VLAGYAQMGVPIEFLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPANVLDA 240

Query: 241 AAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAF 300
           AAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGY+FMPLAF
Sbjct: 241 AAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYVFMPLAF 300

Query: 301 LIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADG-------------GMIVAD 347
           LIGVPWNEALVAGSFIGQKI+VNEFVAYLNFAPY+ + A                + VA+
Sbjct: 301 LIGVPWNEALVAGSFIGQKIIVNEFVAYLNFAPYISEAATACTSVAAEVVKGSLPLCVAE 360

Query: 348 TGLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANL 407
           T   MT RT+AI+SFALCGFANLSSIAILLGGLGAMAPNRRHDLAK+GIRAVIAGSLANL
Sbjct: 361 TQAVMTSRTQAIVSFALCGFANLSSIAILLGGLGAMAPNRRHDLAKMGIRAVIAGSLANL 420

Query: 408 MSATIAGLFLAI 419
           MSATIAGLFLAI
Sbjct: 421 MSATIAGLFLAI 432


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: 833
Number of extensions: 29
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: 432
Length adjustment: 32
Effective length of query: 387
Effective length of database: 400
Effective search space:   154800
Effective search space used:   154800
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: 51 (24.3 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