GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proP in Pseudomonas fluorescens FW300-N2E3

Align Ectoine/proline transporter ProP (characterized)
to candidate AO353_26710 AO353_26710 citrate-proton symporter

Query= SwissProt::Q79VC4
         (504 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_26710 AO353_26710
           citrate-proton symporter
          Length = 434

 Score =  211 bits (536), Expect = 5e-59
 Identities = 133/426 (31%), Positives = 214/426 (50%), Gaps = 21/426 (4%)

Query: 32  AIKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGGLV 91
           AI     GNF+E +DF ++G+    + A F     +   L+     F   +L+RPLG ++
Sbjct: 18  AIFRVTSGNFLEQFDFFLFGFYATYIAAAFFPASSEFASLMMTFAVFGAGFLMRPLGAVI 77

Query: 92  LGPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEY 151
           LG   D VGR+K L VT+++MA  T LI L+P   +IG +A  L+ + +++QGFS G E 
Sbjct: 78  LGAYIDDVGRRKGLIVTLSIMASGTILIVLVPGYETIGLFAPALVLIGRLLQGFSAGAEL 137

Query: 152 AGATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASV-VAITTWVTTHFYGATAMEDFGW 210
            G + Y+AE A   R+GFF ++      +     A++  A+  W+      AT + D+GW
Sbjct: 138 GGVSVYLAEIATPGRKGFFTSWQSASQQVAIVVAAALGYALNQWMP-----ATVVADWGW 192

Query: 211 RIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWR 270
           RIPF     +      LR  + ET  F   +  P            +   + G +  +W+
Sbjct: 193 RIPFFVGCMIVPFIFLLRRSLEETAEFTARRHRP------------SMRQVFGTLLQNWQ 240

Query: 271 PLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWS 330
            ++ G+ +VA T TA Y +T Y P + +  + L ++ A  VT+ + V     LP  G  S
Sbjct: 241 IVIAGMLMVALTTTAFYLITVYAPTFGKTVLHLSTSDALLVTLLVGVSNFCWLPLGGALS 300

Query: 331 DRVGRKPVYATAVAATLILMVPA--FLIMNTGTIGAVLIALSMVAIPTGLYVALSASALP 388
           DR+GR+PV       TL    PA  +L+     I  +L+ L +  I  GLY     +AL 
Sbjct: 301 DRIGRRPVLVAMTLLTLATAYPALTYLVQAPSFINMLLVLLWLSFI-YGLYNGAMVAALT 359

Query: 389 ALFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIAGVALL 448
            + P   R +G  ++Y+++ ++FGG TP I+ FL+Q +G    P  ++ F +  A  A L
Sbjct: 360 EIMPVEVRVAGFSLAYSLATAVFGGFTPAISTFLIQYSGDKAAPGYWMSFAALCALCATL 419

Query: 449 FMTESS 454
           ++   S
Sbjct: 420 YLYRRS 425


Lambda     K      H
   0.322    0.138    0.407 

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: 578
Number of extensions: 37
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: 504
Length of database: 434
Length adjustment: 33
Effective length of query: 471
Effective length of database: 401
Effective search space:   188871
Effective search space used:   188871
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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