GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC in Klebsiella michiganensis M5al

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 BWI76_RS04125 BWI76_RS04125 NupC/NupG family nucleoside CNT transporter

Query= TCDB::Q9KPL5
         (418 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS04125 BWI76_RS04125 NupC/NupG
           family nucleoside CNT transporter
          Length = 425

 Score =  577 bits (1487), Expect = e-169
 Identities = 295/424 (69%), Positives = 352/424 (83%), Gaps = 7/424 (1%)

Query: 1   MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60
           M + M LIGM VLL IAVLLSSNRKAINLRTV GA+ IQ  +GA ILYVP G+  L   S
Sbjct: 1   MQIIMGLIGMVVLLAIAVLLSSNRKAINLRTVLGAWIIQVGIGALILYVPAGRTALLAMS 60

Query: 61  DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120
           + V+NVI YGN+G  F+FGGLVS KMFEVFGGGGF+FA RVLP ++FFS+LI+VLYYLG+
Sbjct: 61  NGVANVIAYGNEGIGFIFGGLVSDKMFEVFGGGGFVFALRVLPVIVFFSSLIAVLYYLGI 120

Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180
           MQ+VIRILGG L+  L TSR ES+SA ANIFVGQTEAPLVVRP++  MT+SELFAVMCGG
Sbjct: 121 MQFVIRILGGALRAVLKTSRTESLSATANIFVGQTEAPLVVRPYIATMTRSELFAVMCGG 180

Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240
           LAS+AG VLAGYA MGV +EYL+AASFMAAPGGLLFAK+++PETE+P+DN  +  +  D 
Sbjct: 181 LASVAGSVLAGYAQMGVPLEYLIAASFMAAPGGLLFAKIIVPETEQPRDNPAMEKNDADP 240

Query: 241 K-PANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLL 299
           + PANV+DAAA GA++G+QLALNVGAML+AFI LIAL+NG+L G+GGWF  P+L L+M+L
Sbjct: 241 QAPANVLDAAASGAASGMQLALNVGAMLLAFIALIALVNGILSGVGGWFNHPDLSLQMIL 300

Query: 300 GWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYL---TEAAPV---VLSE 353
           GW+F+PLA++IGVPWNEATVAG FIG K + NEFVAY  F  YL   TE A     V+S 
Sbjct: 301 GWVFSPLAWVIGVPWNEATVAGSFIGQKLIINEFVAYMNFGEYLKADTEVAAAGLQVIST 360

Query: 354 KTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAG 413
            TKAIISFALCGFANLSSIAIL+GGLG +AP RR +IA++G++AV AGTLSNLM+ATIAG
Sbjct: 361 HTKAIISFALCGFANLSSIAILIGGLGGMAPNRRQEIAQLGMRAVAAGTLSNLMSATIAG 420

Query: 414 FFLS 417
            FL+
Sbjct: 421 VFLA 424


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: 642
Number of extensions: 28
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: 418
Length of database: 425
Length adjustment: 32
Effective length of query: 386
Effective length of database: 393
Effective search space:   151698
Effective search space used:   151698
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 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