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 Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system (characterized)
to candidate 5210585 Shew_3013 sodium/proline symporter (RefSeq)

Query= SwissProt::O06493
         (492 letters)



>FitnessBrowser__PV4:5210585
          Length = 498

 Score =  532 bits (1370), Expect = e-155
 Identities = 265/481 (55%), Positives = 365/481 (75%), Gaps = 6/481 (1%)

Query: 7   ISLGIYFIAMLLIGWYAFKKTTD-INDYMLGGRGLGPFVTALSAGAADMSGWMLMGVPGA 65
           ISL IYF+AML IG +A++++TD ++ Y+LGGR + P VTALSAGA+DMSGWMLMG+PGA
Sbjct: 7   ISLAIYFLAMLAIGLFAYRRSTDDVSGYILGGRQVSPQVTALSAGASDMSGWMLMGLPGA 66

Query: 66  MFATGLSTLWLALGLTIGAYSNYLLLAPRLRAYTEAADDAITIPDFFDKRFQHSSSLLKI 125
           MF  G  T+++ALGL +GA  NYL++AP+LR YTE A++A+TIP+FF KRF   S  ++I
Sbjct: 67  MFLVGFETIYIALGLLLGALVNYLIVAPKLRVYTEVANNALTIPEFFAKRFHDPSCNVRI 126

Query: 126 VSALIIMIFFTLYTSSGMVSGGRLFESAFGADYKLGLFLTTAVVVLYTLFGGFLAVSLTD 185
           +SA II+IFFTLYTS+G+V+GG+LFESAF  +Y+LGL +T  VVV YTL GGFLAVSLTD
Sbjct: 127 ISAAIIVIFFTLYTSAGLVAGGKLFESAFEVNYELGLVITLGVVVSYTLLGGFLAVSLTD 186

Query: 186 FVQGAIMFAALVLVPIVAFTHVGGVAPTFHEIDAVNPHLLDIFKGASVISIISYLAWGLG 245
           FVQG IMF AL+LVP+VA+          +      PH  +  +  +++ +IS L+WGLG
Sbjct: 187 FVQGCIMFVALILVPVVAYQEFSNADKMMNFAYESIPHFGEAMQNVTLLGLISALSWGLG 246

Query: 246 YYGQPHIIVRFMAIKDIKDLKPARRIGMSWMIITVLGSVLTGLIGVAYAHKFGVAVKDPE 305
           Y+GQPHIIVRFMAI+ + D+K A+ IGMSWM +T++G++ TGL+G+AYA+KF + + DPE
Sbjct: 247 YFGQPHIIVRFMAIRSVSDIKTAKNIGMSWMTVTIIGALATGLVGIAYANKFDMKLSDPE 306

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

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

Query: 426 AAMIVGAATVLIWI-----TTGLAKSTGVYEIIPGFILSMIAGIIVSMITKRPAKASYRL 480
           A ++ GAATVL WI       G A S+ +YE+IPGF+ S +    VS +   P + +   
Sbjct: 427 AGIVAGAATVLFWIYAPVLPEGKALSSMLYEMIPGFMASSLVIWGVSALDGDPCENTIET 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: 752
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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Protein sequences (fasta format)
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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