Alignments for a candidate for actP in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Dechlorosoma suillum PS

Align Sodium: solute symporter family protein (characterized, see rationale)
to candidate Dsui_2006 Dsui_2006 putative sodium:solute symporter, VC_2705 subfamily

Query= uniprot:E4PHQ0
         (588 letters)



>FitnessBrowser__PS:Dsui_2006
          Length = 680

 Score =  224 bits (570), Expect = 1e-62
 Identities = 138/341 (40%), Positives = 187/341 (54%), Gaps = 35/341 (10%)

Query: 244 KLNMVLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYLTAPAVASMAR 303
           +LN +     LM+GTA LPHV++R++T P V +AR S  W+L FI LLY TAPA A  A+
Sbjct: 369 RLNFLTLMFCLMVGTAALPHVLMRYYTTPTVKEARESVTWSLFFILLLYFTAPAYAVFAK 428

Query: 304 LNLMTTIYPDGTSAEPIQYDERPNWIKEWEITGLIQFTDKNEDGRIQLYNDSEAFAPTAE 363
             + +T+        PI +   P+W+  W   GL+   D N DG +QL            
Sbjct: 429 YEVYSTLINT-----PIAH--LPSWVAAWGKVGLVAIEDINHDGLLQLA----------- 470

Query: 364 ARGWNGNELVVNRDILVLANPEIANLPGWVIGLIAAGGLAAALSTAAGLLLAISSAVSHD 423
                  EL +N D++VLA PEIA LP  + GL+AAGGLAAALSTA GLLL I+ ++SHD
Sbjct: 471 -------ELSLNPDVIVLATPEIAGLPYVISGLVAAGGLAAALSTADGLLLTIAGSLSHD 523

Query: 424 LIKGSINPAISEKGELLAARISMAVAIVVATYLGANPPGFAAQVVALAFGIAAASLFPAL 483
           +    I P  S +  L+ ++  + V  V+A  + A  P     +VA AF IAAA+ FPAL
Sbjct: 524 VYYKIIQPRASTQWRLVISKSLLLVTAVLAATVAAQRPATILYMVAWAFSIAAAAFFPAL 583

Query: 484 MMGIFSKRVNNTGAIAGMLSGLTFTLVYI----FVYKGWLFIPGTNNLPDTPDNWVLGIS 539
           ++GIF KR N  GA++GM+ GL  T+ Y+    F    WL + G    P     W  GI 
Sbjct: 584 VIGIFWKRANRAGAVSGMVVGLLITVYYMVRVQFDSVPWLGLRGIGMEP-----W-FGIQ 637

Query: 540 PLSIGAIGAIVNFAVAFIVSNATEEPPVEIQELVESVRYPR 580
             S G  G    F    +VS  T+ P  E+Q+ VE V YP+
Sbjct: 638 STSAGVWGVPAGFLTIVVVSLLTKPPSREVQDFVEQVHYPQ 678



 Score =  195 bits (496), Expect = 4e-54
 Identities = 91/203 (44%), Positives = 131/203 (64%)

Query: 6   INIIFVGGSFLLYIAIAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGL 65
           I   F+  + L+Y  I + ++    S++YVAG  V  + NG A GADWMSAASFI MAG 
Sbjct: 42  IGYAFLLFTILIYATIGVMSRTADVSEYYVAGRRVPALFNGMATGADWMSAASFIGMAGT 101

Query: 66  IAAGGYANSTFLMGWTGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNARLVAVICLI 125
           +   GY    ++MGWTGGYVL+A+ LAPYLRKFG++T+P+F+  R+     RLV V   I
Sbjct: 102 LYLTGYQGLAYIMGWTGGYVLVALFLAPYLRKFGQYTIPDFLAVRYGGNAPRLVGVAAAI 161

Query: 126 VASVTYVIGQMAGAGVAFSRFLEVDSTVGLMIAAVVVFVYAVMGGMKGITYTQVAQYCVL 185
           +AS  YV+ Q+ G G+  SRF+ +   +G+ +    + V + +GGM+ +T+TQVAQY +L
Sbjct: 162 IASFVYVVAQIYGVGLITSRFVSLQFEIGVFVGLAGILVCSFLGGMRAVTWTQVAQYVIL 221

Query: 186 IVAYTIPAVFISLQLTGNPIPGL 208
           I+AY  P   +S Q+T  P+P L
Sbjct: 222 IIAYVTPVALLSFQITSVPVPQL 244


Lambda     K      H
   0.323    0.138    0.413 

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: 1033
Number of extensions: 72
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 588
Length of database: 680
Length adjustment: 38
Effective length of query: 550
Effective length of database: 642
Effective search space:   353100
Effective search space used:   353100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 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