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

GapMind for catabolism of small carbon sources

Alignments 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)



>FitnessBrowser__MR1:200392
          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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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