GapMind for catabolism of small carbon sources

 

Aligments for a candidate for LAT2 in Dyella japonica UNC79MFTsu3.2

Align Serine/threonine exchanger SteT (characterized)
to candidate N515DRAFT_4009 N515DRAFT_4009 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= SwissProt::O34739
         (438 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4009 N515DRAFT_4009 amino
           acid/polyamine/organocation transporter, APC superfamily
           (TC 2.A.3)
          Length = 445

 Score =  210 bits (535), Expect = 6e-59
 Identities = 128/430 (29%), Positives = 217/430 (50%), Gaps = 6/430 (1%)

Query: 3   TEDNGLKKEIGLLFALTLVIGTIIGSGVFMKPGAVLAYSGDSKMALFAWLLGGILTLAGG 62
           T  +G  + +    A  +V+G IIG G+F+ PG     +      L  W+  G+LTL G 
Sbjct: 4   TPASGYMRRLTSWDAAMIVVGGIIGGGIFLNPGIAAQRTESGLALLLVWVGAGVLTLIGA 63

Query: 63  LTIAEIGTQIPKTGGLYTYLEEVYGEFWGFLCGWVQIIIYGPAIIGALGLYFGSLMANLF 122
           L  AE+G + P  GG Y YL E +G   GFL GW  +++       A+   F S  + +F
Sbjct: 64  LCYAELGARRPHAGGSYVYLREAFGSLAGFLFGWTMLLVIYSGSAAAVATIFASYASGVF 123

Query: 123 GWGSGLSKVIGIIAVLFLCVINIIGTKYGGFVQTLTTIGKLIPIACIIVFGLW--KGDQH 180
           G   G  K +   A++F+  IN+ G K G  VQ L T+ KL+ +A ++V GL+    D  
Sbjct: 124 GLPPGTIKPLAAGALVFVAGINLFGLKLGAQVQNLFTLLKLLAVAVLVVCGLFLAGADGA 183

Query: 181 IFTAVNESISDMNFGAAILATLFAYDGWILLAALGGEMKNPEKLLPRAMTGGLLIVTAIY 240
              A + +  ++ F  A L  LFAY G+  L  L GE++ P++ LPRA+  G+L V  +Y
Sbjct: 184 GVLASDPARGNVGFIGAALPVLFAYSGFTYLNNLAGEVREPQRTLPRALFFGMLAVIVVY 243

Query: 241 IFINFALLHILSANEIVTLGENATSTAATMLFGSIGGKLISVGIIVSIFGCLNGKVLSFP 300
             +N A L +L  ++ +       +   + +FG IG K+I++GI VS  G  N  +++  
Sbjct: 244 ALVNVAYLAVL-GHDGLARSNTPAADVMSRVFGPIGAKVIAIGIAVSTLGFCNITLVAGA 302

Query: 301 RVSFAMAERKQLPFAEKLSHVHPSFRTPWIAISFQIALALIMMLISNPDKLSEISIFMIY 360
           RV   M +     F   ++ +HP  RTP +A+      A+ + +  N  +L + + F  +
Sbjct: 303 RVLQVMGDDGL--FFRNVARLHPRHRTPNVALLLLSGWAVFLAMAFNFGQLLDYATFGDW 360

Query: 361 IFYVMAFFAVFILRKRAKGEKRAYSVPLYPFMPILAIAGSFFVLGSTLITDTMSCGLSIL 420
           +   +    +F  R R KG    + VP YP +P++ +    +++ +TL+   +   + + 
Sbjct: 361 LACAVGVVTIFWYRSRDKG-GADFRVPGYPVLPLIFVGVVGWIVVATLLAKPIQACIVLA 419

Query: 421 IGLAGLPVYY 430
           +   G+PV++
Sbjct: 420 VMAVGIPVFH 429


Lambda     K      H
   0.328    0.145    0.437 

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: 626
Number of extensions: 39
Number of successful extensions: 6
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: 438
Length of database: 445
Length adjustment: 32
Effective length of query: 406
Effective length of database: 413
Effective search space:   167678
Effective search space used:   167678
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 (21.7 bits)
S2: 51 (24.3 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