GapMind for catabolism of small carbon sources

 

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

Align Concentrative nucleoside transporter, CNT, of 418 aas and 12 TMSs. A repeat-swapped model of VcCNT predicts that nucleoside transport occurs via a mechanism involving an elevator-like substrate binding domain movement across the membrane (characterized)
to candidate 200392 SO1214 NupC family protein (NCBI ptt file)

Query= TCDB::Q9KPL5
         (418 letters)



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

 Score =  563 bits (1450), Expect = e-165
 Identities = 291/439 (66%), Positives = 351/439 (79%), Gaps = 30/439 (6%)

Query: 1   MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60
           M++ MSL+G+ VLL I  LLS+N+KAINLRTVGGA AIQ + G F+LYVP G+++L+G S
Sbjct: 1   MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKGMS 60

Query: 61  DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120
           DAVS+VI +  +G  FLFG L + K+       GFIFA  VLP ++FFS+LI+VLYYLGV
Sbjct: 61  DAVSSVIGFAQNGIGFLFGDLANFKL-------GFIFAVNVLPVIVFFSSLIAVLYYLGV 113

Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180
           MQW+IRI+GGGLQKALGTSR ESMSA ANIFVGQTEAPLVVRPF+P MTQSELFAVM GG
Sbjct: 114 MQWIIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAVMVGG 173

Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240
           LASIAG VLAGYA MGV IE+LVAASFMAAPGGLL AKLM PETE  +++ D  L    D
Sbjct: 174 LASIAGSVLAGYAQMGVPIEFLVAASFMAAPGGLLMAKLMHPETEVAKNDMD-ELPEDPD 232

Query: 241 KPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLG 300
           KPANV+DAAA GAS+G+ LALNVGAML+AF+GLIA+ING++GG+GGWFG+  L LE++LG
Sbjct: 233 KPANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILG 292

Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAA------------- 347
           ++F PLAFLIGVPWNEA VAG FIG K + NEFVAY  FAPY++EAA             
Sbjct: 293 YVFMPLAFLIGVPWNEALVAGSFIGQKIIVNEFVAYLNFAPYISEAATACTSVAAEVVKG 352

Query: 348 ---------PVVLSEKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAV 398
                      V++ +T+AI+SFALCGFANLSSIAILLGGLG++AP RR D+A+MG++AV
Sbjct: 353 SLPLCVAETQAVMTSRTQAIVSFALCGFANLSSIAILLGGLGAMAPNRRHDLAKMGIRAV 412

Query: 399 IAGTLSNLMAATIAGFFLS 417
           IAG+L+NLM+ATIAG FL+
Sbjct: 413 IAGSLANLMSATIAGLFLA 431


Lambda     K      H
   0.325    0.141    0.414 

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: 661
Number of extensions: 35
Number of successful extensions: 5
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: 418
Length of database: 432
Length adjustment: 32
Effective length of query: 386
Effective length of database: 400
Effective search space:   154400
Effective search space used:   154400
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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