GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC in Shewanella amazonensis SB2B

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 6936789 Sama_0971 nucleoside transporter (RefSeq)

Query= TCDB::Q9KPL5
         (418 letters)



>lcl|FitnessBrowser__SB2B:6936789 Sama_0971 nucleoside transporter
           (RefSeq)
          Length = 419

 Score =  575 bits (1482), Expect = e-169
 Identities = 296/426 (69%), Positives = 350/426 (82%), Gaps = 17/426 (3%)

Query: 1   MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60
           MS+ MSL+G+AVLLGI  LLS+N+KAI++R VGGA AIQ + G F+LYVPWG+++L+  S
Sbjct: 1   MSILMSLVGVAVLLGIGFLLSNNKKAISVRAVGGALAIQAAFGGFVLYVPWGKDILKTVS 60

Query: 61  DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120
           D VS VI YG +G +FLFG L   K+       GFIFA  VLP +IFFS+LI+VLYYLG+
Sbjct: 61  DGVSAVIGYGQNGINFLFGDLAQFKV-------GFIFAINVLPVIIFFSSLIAVLYYLGI 113

Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180
           MQWVIRI+GGGLQKALGTSR ESMSA ANIFVGQTEAPLVVRPF+P MTQSELFA+M GG
Sbjct: 114 MQWVIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGG 173

Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240
           LASIAG VLAGYASMGVKIEYLVAASFMAAPGGLL AKLM PETE  + NE   L    D
Sbjct: 174 LASIAGSVLAGYASMGVKIEYLVAASFMAAPGGLLMAKLMHPETENTK-NEMDELPEDPD 232

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

Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAP---------VVL 351
           ++F PLAFLIGVPWNEA VAG FIG K V NEFVAY  FAPYL + A            +
Sbjct: 293 YIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGIVVAETGAAM 352

Query: 352 SEKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATI 411
           S++TKAI+SFALCGFANLSSIAILLGGLG++AP RR D+A++G++AVIAG+L+NLM+AT+
Sbjct: 353 SDRTKAIVSFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATL 412

Query: 412 AGFFLS 417
           AG FL+
Sbjct: 413 AGLFLA 418


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: 684
Number of extensions: 38
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: 419
Length adjustment: 32
Effective length of query: 386
Effective length of database: 387
Effective search space:   149382
Effective search space used:   149382
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