GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putP in Shewanella sp. ANA-3

Align Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system (characterized)
to candidate 7026926 Shewana3_4055 sodium/proline symporter (RefSeq)

Query= SwissProt::O06493
         (492 letters)



>lcl|FitnessBrowser__ANA3:7026926 Shewana3_4055 sodium/proline
           symporter (RefSeq)
          Length = 498

 Score =  545 bits (1405), Expect = e-159
 Identities = 272/481 (56%), Positives = 368/481 (76%), Gaps = 6/481 (1%)

Query: 7   ISLGIYFIAMLLIGWYAFKKTTD-INDYMLGGRGLGPFVTALSAGAADMSGWMLMGVPGA 65
           +SL IYFIAML IG +A++K+TD ++ Y+LGGR + P VTALSAGA+DMSGWMLMG+PGA
Sbjct: 7   VSLAIYFIAMLAIGLFAYRKSTDDVSGYILGGRQVSPHVTALSAGASDMSGWMLMGLPGA 66

Query: 66  MFATGLSTLWLALGLTIGAYSNYLLLAPRLRAYTEAADDAITIPDFFDKRFQHSSSLLKI 125
           MF  G  TL++ALGL IGA  NYL++AP+LR YTE AD+A+TIP+FF KRF  + + ++I
Sbjct: 67  MFLVGFETLYIALGLLIGALINYLVVAPKLRVYTEVADNALTIPEFFAKRFGQADNSIRI 126

Query: 126 VSALIIMIFFTLYTSSGMVSGGRLFESAFGADYKLGLFLTTAVVVLYTLFGGFLAVSLTD 185
           ++A II+IFFTLYTS+G+V+GG+LFESAFG +Y +GL +T AVVV YTL GGFLAVSLTD
Sbjct: 127 IAAAIIVIFFTLYTSAGLVAGGKLFESAFGLNYDIGLVVTLAVVVSYTLLGGFLAVSLTD 186

Query: 186 FVQGAIMFAALVLVPIVAFTHVGGVAPTFHEIDAVNPHLLDIFKGASVISIISYLAWGLG 245
           FVQG IMF ALVLVP VA+          +      PH  D  +  +++ +IS L+WGLG
Sbjct: 187 FVQGCIMFVALVLVPFVAYQEFTSADRMMNFAYQSIPHFTDAMQNVTLLGLISSLSWGLG 246

Query: 246 YYGQPHIIVRFMAIKDIKDLKPARRIGMSWMIITVLGSVLTGLIGVAYAHKFGVAVKDPE 305
           Y+GQPHIIVRFMAI+ + D+K ARRIG+SWM +T++G++ TGL+G+AYA+KFG+ + DPE
Sbjct: 247 YFGQPHIIVRFMAIRSVADIKTARRIGISWMTVTIIGALATGLVGIAYANKFGMKLSDPE 306

Query: 306 MIFIIFSKILFHPLITGFLLSAILAAIMSSISSQLLVTASAVTEDLYRSFFRRKASDKEL 365
            IFI+FS++LFHPLI+GFLL+AILAAIMS+ISSQLLV++S++TED+YR+  +++AS++E+
Sbjct: 307 TIFIVFSELLFHPLISGFLLAAILAAIMSTISSQLLVSSSSLTEDIYRTLSKKQASEQEM 366

Query: 366 VMIGRLSVLVIAVIAVLLSLNPNSTILDLVGYAWAGFGSAFGPAILLSLYWKRMNEWGAL 425
           V +GR  V  +A++A LL+L+ +++IL LV  AWAGFG+AFGP +L SLY   +    A+
Sbjct: 367 VKMGRYGVAGVAIVATLLALDRSNSILSLVSNAWAGFGAAFGPLVLFSLYKANLTHKAAI 426

Query: 426 AAMIVGAATVLIWI-----TTGLAKSTGVYEIIPGFILSMIAGIIVSMITKRPAKASYRL 480
           A +I GA TVL WI     + G A S+ VYE+IPGF++S     +VS     P   + + 
Sbjct: 427 AGIISGALTVLFWIYAPVLSDGKALSSLVYEMIPGFVVSSTVIYLVSKFDNDPCAKTTKQ 486

Query: 481 F 481
           F
Sbjct: 487 F 487


Lambda     K      H
   0.328    0.142    0.421 

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: 744
Number of extensions: 42
Number of successful extensions: 4
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: 492
Length of database: 498
Length adjustment: 34
Effective length of query: 458
Effective length of database: 464
Effective search space:   212512
Effective search space used:   212512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 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