GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5210585
          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 (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:

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