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 5209987 Shew_2435 sodium/proline symporter (RefSeq)

Query= SwissProt::P07117
         (502 letters)



>lcl|FitnessBrowser__PV4:5209987 Shew_2435 sodium/proline symporter
           (RefSeq)
          Length = 483

 Score =  509 bits (1311), Expect = e-149
 Identities = 259/494 (52%), Positives = 346/494 (70%), Gaps = 24/494 (4%)

Query: 1   MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60
           M I  P+LVTF  Y+  M+ IG  A+++T + DDYILGGRS+GP VTALS GASDMSGWL
Sbjct: 1   MNIELPILVTFFGYLILMMGIGLWAYKATDSVDDYILGGRSMGPAVTALSVGASDMSGWL 60

Query: 61  LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120
           L+GLPGAV+L G+ E+WI IGL  GAW+NW  VA RLR++T++ +NALTLPD+F  RFED
Sbjct: 61  LLGLPGAVYLGGLGEAWIGIGLVFGAWLNWLFVAKRLRIYTQFTDNALTLPDFFEKRFED 120

Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180
           K  +L+++SA+ IL+FFT Y +SG+V GA LFE  FG+ Y  AL  G+   + YTF+GGF
Sbjct: 121 KQSVLKLVSAVTILVFFTFYTSSGMVGGAILFEKVFGLDYNLALLIGSGIIVAYTFVGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVD--MLKGLN---- 234
            AVSWTD  Q  LM+ AL++ PV +           +   Q  I ++D  ML  L+    
Sbjct: 181 FAVSWTDFFQGCLMLIALLIVPVTIF---------SQPETQNGIHSLDPAMLSLLSDNTT 231

Query: 235 FVAIISLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIA 294
            + + SL+ WGLGYFGQPHIL+RFMA  S   +  +RRI+M+WMI+ L GA+A G  G  
Sbjct: 232 MIGLASLLAWGLGYFGQPHILSRFMAIGSADDLKVSRRIAMSWMIVALMGALATGLAGTL 291

Query: 295 YFNDHPALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAIT 354
           YF D P        N E +FI LA   FNPWI G+L++AIL+A+MST+  QLLVCSS IT
Sbjct: 292 YFADQPI------DNPETIFIHLAHAAFNPWIGGLLVAAILSAIMSTIDSQLLVCSSVIT 345

Query: 355 EDLYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGP 414
           ED YK +LR  AS KEL+ +GR+ VL +A+++  +A NPE+ VL LVSYAWAGFGAAFGP
Sbjct: 346 EDFYKKWLRPDASSKELMMIGRIGVLTIAVISGVIALNPESSVLSLVSYAWAGFGAAFGP 405

Query: 415 VVLFSVMWSRMTRNGALAGMIIGALTVIVWKQF--GWLGLYEIIPGFIFGSIGIVVFSLL 472
           VV+ S+ W   +RNGA+A +I+GA+TV++WKQ   G   LYEI+PGF+F ++  V+ SL+
Sbjct: 406 VVILSLFWRGYSRNGAVATIIVGAITVVLWKQSTGGIFDLYEILPGFLFATLAGVLVSLV 465

Query: 473 GKAPSAAMQKRFAE 486
             AP+ + +++F +
Sbjct: 466 -SAPADSTREQFEQ 478


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: 813
Number of extensions: 38
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: 502
Length of database: 483
Length adjustment: 34
Effective length of query: 468
Effective length of database: 449
Effective search space:   210132
Effective search space used:   210132
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