GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS27055
          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:

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