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

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 5209987 Shew_2435 sodium/proline symporter (RefSeq)

Query= SwissProt::P07117
         (502 letters)



>FitnessBrowser__PV4:5209987
          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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources