GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Shew_2731 in Azospirillum brasilense Sp245

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease

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



>lcl|FitnessBrowser__azobra:AZOBR_RS02940 AZOBR_RS02940 actetate
           permease
          Length = 572

 Score =  180 bits (456), Expect = 2e-49
 Identities = 150/492 (30%), Positives = 226/492 (45%), Gaps = 51/492 (10%)

Query: 19  IGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSFVGYDGSVY 76
           +GI  W+  R  S K+FY AGGG+    NG+A A D+MSAASF+ +AG+V   G+DG ++
Sbjct: 53  LGITYWAARRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIF 112

Query: 77  LMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFICFTYIAGQM 136
            +GW  G+ ++   +A  LR  GK+T  D    R+     RT+A   ++     Y+  QM
Sbjct: 113 SVGWLVGWPIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQM 172

Query: 137 RGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIFAFMVPAIFI 196
            G G +      ++    V I   ++  Y   GGM   T+ Q+ +  +L+          
Sbjct: 173 VGAGKLIQLLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSG-------- 224

Query: 197 SVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSA--QLGFSQYTEGSKGMIDVFF 254
           +  M   +L + GF  E    A  +T V +  K  G+ A   L     +  S GM     
Sbjct: 225 ASFMAFAVLAKFGFSPE----AMFSTAVQVHPKATGIMAPGALITDPVSAISLGM----- 275

Query: 255 ITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIET 314
              ALMFGTAGLPH+++RFFTV   K+AR S  +A  FI   Y     L        I  
Sbjct: 276 ---ALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY----ILTFIIGFGAIVL 328

Query: 315 INGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETN-EMKIDRDIMVLAT 373
           +  P++TG AY                      +  K+  A G+ N  M I    M    
Sbjct: 329 LLAPDATG-AYPFL-------------------DAAKLAAAGGKPNPSMIIGGSNMAAIH 368

Query: 374 PEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPD-ISDKQELLYA 432
              A         ++A   A  L+  AGL L  +++VSHDL          S+  E+  +
Sbjct: 369 TAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVS 428

Query: 433 RIAAALGIVMAGYFGIN-PPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGM 491
           +I   +  +++ + GI      VA +V +AF +AAS+ FP ++M +F   M   GA+ G 
Sbjct: 429 KITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGG 488

Query: 492 VIGLLFSASYII 503
            IGL+ S S +I
Sbjct: 489 WIGLVSSVSLLI 500


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: 931
Number of extensions: 57
Number of successful extensions: 4
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: 572
Length of database: 572
Length adjustment: 36
Effective length of query: 536
Effective length of database: 536
Effective search space:   287296
Effective search space used:   287296
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: 53 (25.0 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:

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