GapMind for catabolism of small carbon sources

 

Aligments for a candidate for L-LDH in Azospirillum brasilense Sp245

Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate AZOBR_RS27055 AZOBR_RS27055 L-lactate dehydrogenase

Query= reanno::WCS417:GFF3737
         (376 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS27055 AZOBR_RS27055 L-lactate
           dehydrogenase
          Length = 384

 Score =  241 bits (616), Expect = 2e-68
 Identities = 136/369 (36%), Positives = 198/369 (53%), Gaps = 7/369 (1%)

Query: 7   SDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSLKTTLFG 66
           ++ R  A+ +LPR LF+YID GA  E  +  + + L  +  + R+L +V      T LFG
Sbjct: 10  AEARQRARARLPRGLFEYIDRGAEDETGIATSKTALDSLVFKPRVLVDVSKRDATTRLFG 69

Query: 67  QELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQSAQAIWF 126
            +  MP++++P  + G+    GEV+ AKAAA  GIPFC+ST S+  +E +A +S   +WF
Sbjct: 70  VDQPMPLVVAPTAVAGLVWYDGEVELAKAAAAVGIPFCVSTQSITSVERIAGESGARLWF 129

Query: 127 QLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPFAAQRRM-LQA 185
           QLYV + R   R  + RA+ AG   LV TVD      R  +  +G   P     R  L  
Sbjct: 130 QLYVWRSRERTRELVRRAERAGAEALVLTVDTAVTPNREYNVRNGFGIPIKPSVRAGLDC 189

Query: 186 VTKPQWAFDVGLMGRPHDLGNISKYLGKPTHLEDYIGWLANNFDASIS----WKDLEWIR 241
           +  P+W    G+  +    G +  Y   P      +G +A   +  ++    W D+  +R
Sbjct: 190 LAHPRWF--AGVFAKYLRNGGVPTYAHYPDEFRTALGRVAVGDEIGLAQDVGWGDVRSLR 247

Query: 242 EFWKGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADAVGDDL 301
           + WKG +I+KG+L   DA+ A   G DGIVVSNHG R LD  +   + L  IA+ VGD +
Sbjct: 248 DAWKGKLILKGVLRADDAEKAAELGVDGIVVSNHGARNLDHAIHPVRCLTDIAERVGDRV 307

Query: 302 TVLVDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMRVAMTL 361
           TVL DSG+R G  V   L LGA+  LLGRA  Y LA DG  G + +L++  +E+   M  
Sbjct: 308 TVLADSGVRRGSHVAGYLGLGAQGVLLGRAVLYGLATDGAAGAQAVLEMIRRELLTTMGF 367

Query: 362 TGVTSIAQI 370
            G  ++A I
Sbjct: 368 LGAPTVADI 376


Lambda     K      H
   0.321    0.136    0.401 

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: 348
Number of extensions: 17
Number of successful extensions: 2
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: 376
Length of database: 384
Length adjustment: 30
Effective length of query: 346
Effective length of database: 354
Effective search space:   122484
Effective search space used:   122484
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: 50 (23.9 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