Alignments for a candidate for Shew_2731 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for Shew_2731 in Acidovorax sp. GW101-3H11

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate Ac3H11_204 Acetate permease ActP (cation/acetate symporter)

Query= reanno::PV4:5209923
         (572 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_204
          Length = 699

 Score =  187 bits (474), Expect = 2e-51
 Identities = 108/298 (36%), Positives = 168/298 (56%), Gaps = 16/298 (5%)

Query: 259 LMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIETINGP 318
           LM GTAGLPH++ RF+T P V  AR S GW+L FIA++Y + PALA   +  +++ +   
Sbjct: 403 LMVGTAGLPHLLTRFYTSPSVSAARASVGWSLFFIALLYLSAPALAVLVKFEVMQNL--- 459

Query: 319 ESTGVAYETAPDWIKNWEK--TGLIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLATPEI 376
              G ++E  P W+  W +  + L+  +D N DG I +      E+++  D+++LATPE+
Sbjct: 460 --VGSSFEALPTWMAQWSRVDSSLLSLEDVNGDGLIQFG-----EIRLGADLIMLATPEL 512

Query: 377 ANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAA 436
             LP  V  LVAAGGLAAALST+ GLLL IS ++  DL  ++     S +Q ++ ++ A 
Sbjct: 513 GGLPYVVSGLVAAGGLAAALSTADGLLLTISNALVRDLYFQDSQRKASPEQRVILSKFAL 572

Query: 437 ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGL- 495
               + A +     P  +  +V+ +F LAAS+  PA+++GIF R   ++GA+AGM+ GL 
Sbjct: 573 LAVALSAAFVAALKPSEILPMVSASFSLAASAFVPAMVLGIFWRGTTRQGAVAGMLTGLG 632

Query: 496 ---LFSASYIIYFKFVNPGDNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVP 550
               +  S++   + V P    A    FGI P   G+ G+     V  ++S +T   P
Sbjct: 633 IAVYYMLSHVPAVQGVLPRWLLADGLWFGIQPISAGVFGVPCGLLVTVVLSWMTRPAP 690



 Score =  184 bits (467), Expect = 1e-50
 Identities = 88/208 (42%), Positives = 134/208 (64%), Gaps = 7/208 (3%)

Query: 14  TFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSFVGYDG 73
           T  +Y GI ++ R    +++YVAG  + P+ NGMATAADWMSAASFISL+G +   G+ G
Sbjct: 58  TVMVYAGIGVYGRTTDPEDYYVAGRRIPPMYNGMATAADWMSAASFISLSGALYLQGFSG 117

Query: 74  S-------VYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIF 126
           +        YL+GWTGG+ L+A+ +AP+LR  G +T+PDF   R+  +  R +A + A+ 
Sbjct: 118 TPGQAGGLAYLLGWTGGFCLVAMLIAPHLRAMGLYTIPDFFHVRFGGRWPRVIAALAAVL 177

Query: 127 ICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLI 186
             FTY+  Q+ GVG++ SR   V+ + G+ +G+  V   + LGGM+ IT+TQVAQY VL+
Sbjct: 178 CSFTYVVAQIYGVGLIASRLTGVQFEIGIMLGLGGVLLCSFLGGMRAITWTQVAQYVVLL 237

Query: 187 FAFMVPAIFISVMMTGHILPQLGFGAEL 214
            AFM+P  +++    G+ L  L +G ++
Sbjct: 238 LAFMIPVSWLAYKQLGNPLAPLVYGEQI 265


Lambda     K      H
   0.326    0.140    0.423 

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: 1043
Number of extensions: 48
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 572
Length of database: 699
Length adjustment: 38
Effective length of query: 534
Effective length of database: 661
Effective search space:   352974
Effective search space used:   352974
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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