GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putP in Shewanella loihica PV-4

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 5210585 Shew_3013 sodium/proline symporter (RefSeq)

Query= SwissProt::P07117
         (502 letters)



>lcl|FitnessBrowser__PV4:5210585 Shew_3013 sodium/proline symporter
           (RefSeq)
          Length = 498

 Score =  415 bits (1067), Expect = e-120
 Identities = 231/489 (47%), Positives = 314/489 (64%), Gaps = 15/489 (3%)

Query: 9   VTFCVYIFGMILIGFIAWR-STKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPGA 67
           ++  +Y   M+ IG  A+R ST +   YILGGR + P VTALSAGASDMSGW+LMGLPGA
Sbjct: 7   ISLAIYFLAMLAIGLFAYRRSTDDVSGYILGGRQVSPQVTALSAGASDMSGWMLMGLPGA 66

Query: 68  VFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILRI 127
           +FL G    +IA+GL LGA +N+ +VA +LRV+TE  NNALT+P++F  RF D S  +RI
Sbjct: 67  MFLVGFETIYIALGLLLGALVNYLIVAPKLRVYTEVANNALTIPEFFAKRFHDPSCNVRI 126

Query: 128 ISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWTD 187
           ISA +I++FFT+Y ++G+VAG +LFES F ++YE  L       + YT +GGFLAVS TD
Sbjct: 127 ISAAIIVIFFTLYTSAGLVAGGKLFESAFEVNYELGLVITLGVVVSYTLLGGFLAVSLTD 186

Query: 188 TVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENV-DMLKGLNFVAIISLMGWGL 246
            VQ  +M  ALIL PV+         D +     +SI +  + ++ +  + +IS + WGL
Sbjct: 187 FVQGCIMFVALILVPVVAYQEFSN-ADKMMNFAYESIPHFGEAMQNVTLLGLISALSWGL 245

Query: 247 GYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPALAGAV 306
           GYFGQPHI+ RFMA  S   I  A+ I M+WM + + GA+A G  GIAY N         
Sbjct: 246 GYFGQPHIIVRFMAIRSVSDIKTAKNIGMSWMTVTIIGALATGLVGIAYANKFDMKL--- 302

Query: 307 NQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAFLRKHA 366
             + E +FI  +++LF+P I+G LL+AILAA+MST+S QLLV SS++TED+Y+   +K A
Sbjct: 303 -SDPETIFIVFSELLFHPLISGFLLAAILAAIMSTISSQLLVSSSSLTEDIYRVVSKKEA 361

Query: 367 SQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVMWSRMT 426
           S++E+V +GR  V  VA+VA  LA +  N +L LVS AWAGFGAAFGP+VLFS+    +T
Sbjct: 362 SEEEMVKLGRFGVAGVAIVASLLALDRSNSILSLVSNAWAGFGAAFGPLVLFSLYKKNLT 421

Query: 427 RNGALAGMIIGALTVIVWKQFGWLG--------LYEIIPGFIFGSIGIVVFSLLGKAPSA 478
              A+AG++ GA TV+ W     L         LYE+IPGF+  S+ I   S L   P  
Sbjct: 422 HKAAVAGIVAGAATVLFWIYAPVLPEGKALSSMLYEMIPGFMASSLVIWGVSALDGDPCE 481

Query: 479 AMQKRFAEA 487
              + F EA
Sbjct: 482 NTIETFDEA 490


Lambda     K      H
   0.328    0.140    0.436 

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: 704
Number of extensions: 34
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 502
Length of database: 498
Length adjustment: 34
Effective length of query: 468
Effective length of database: 464
Effective search space:   217152
Effective search space used:   217152
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