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 202800 SO3706 NupC family protein (NCBI ptt file)

Query= TCDB::Q9KPL5
         (418 letters)



>lcl|FitnessBrowser__MR1:202800 SO3706 NupC family protein (NCBI ptt
           file)
          Length = 422

 Score =  509 bits (1312), Expect = e-149
 Identities = 254/422 (60%), Positives = 331/422 (78%), Gaps = 7/422 (1%)

Query: 1   MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60
           M + +SL+G+  LL +A L S NR+AIN RTVG AF +Q +LGAF++Y   GQ ++   +
Sbjct: 1   MQILVSLLGIITLLAVAYLASENRRAINYRTVGLAFLLQLALGAFVMYSALGQSMIFSMA 60

Query: 61  DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120
            AVSNVI+Y NDG SF+FGGLVS KM+E+FG GGF+ AF+VLP ++FFSAL +VLYYLG+
Sbjct: 61  AAVSNVISYSNDGMSFMFGGLVSDKMYELFGAGGFVIAFKVLPIIVFFSALSAVLYYLGI 120

Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180
           MQ V++ +GG LQK L TS+AESMSA+ANIF+G TEAPL+++P++P+MT+SELFAVMCGG
Sbjct: 121 MQLVVKAVGGALQKLLNTSKAESMSASANIFLGVTEAPLLIKPYMPRMTRSELFAVMCGG 180

Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240
           LASIAG +LAGYA +G+K+EYL+AASFMAAPGGLLFAKL++P+TE   D      +  ++
Sbjct: 181 LASIAGTMLAGYAQLGIKMEYLLAASFMAAPGGLLFAKLLIPQTETINDAHLQLTE--EN 238

Query: 241 KPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLG 300
           +P N++DAA  G  +GL LAL VGAML +FI L+AL NGMLGGIG WFG+  L L+ +LG
Sbjct: 239 QPRNLLDAATTGTMSGLSLALAVGAMLFSFISLVALFNGMLGGIGAWFGLEGLTLQQILG 298

Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVV-----LSEKT 355
           +LFAPLA+L+G+ WNEA +AG FIG K V NEF AY   APYL+  A V      +SE+T
Sbjct: 299 YLFAPLAWLMGISWNEAMLAGSFIGQKIVINEFFAYINLAPYLSGDALVATTGQPMSERT 358

Query: 356 KAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFF 415
           + I+SFALCGFAN+ ++AI + G+G L P+RR +IA +G+KA+ AG LSNLMAATIAG F
Sbjct: 359 QVILSFALCGFANIGTVAIAIAGIGGLVPERRAEIASLGLKALAAGILSNLMAATIAGLF 418

Query: 416 LS 417
           +S
Sbjct: 419 MS 420


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: 632
Number of extensions: 30
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: 422
Length adjustment: 32
Effective length of query: 386
Effective length of database: 390
Effective search space:   150540
Effective search space used:   150540
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