GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Dyella japonica UNC79MFTsu3.2

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3307
          Length = 426

 Score =  175 bits (444), Expect = 2e-48
 Identities = 122/370 (32%), Positives = 175/370 (47%), Gaps = 30/370 (8%)

Query: 3   SNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVL 53
           +N EL QR  Q +P GV             P F  RA+   +WDVEG+ Y+D+ G    +
Sbjct: 2   TNHELFQRAKQLMPGGVNSPVRAFKSVGGEPFFTARADGAYLWDVEGKRYIDYVGSWGPM 61

Query: 54  NTGHLHPKVVAAVEAQLK---KLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTT 110
             GH HP+V  AVE  +K        C         + + E + + VP        +V +
Sbjct: 62  IVGHNHPRVREAVERAVKDGLSFGTPC------PAEITMAETITRLVPS--VDMVRMVNS 113

Query: 111 GSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRAL 170
           G+EA  +A+++AR AT RS  + F G YHG     L   G     + G+   PG V +A 
Sbjct: 114 GTEATMSAIRLARGATGRSKIVKFEGCYHGHGDSFLVKAGS-GALTFGVPTSPG-VPKAA 171

Query: 171 YPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCD 230
               L     D  +A+   +F    A  DIA ++IEPV G          ++Q LRALC 
Sbjct: 172 ADLTLTLAYND--LAAAEALFAEHGA--DIAGLIIEPVAGNMNCIPPKDGYLQGLRALCT 227

Query: 231 EHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVA 290
            HG +LI DEV +G  R     A    G+ PDL+TF K I GG P+    GR E+M+ +A
Sbjct: 228 RHGALLIFDEVMTGF-RVALGGAQAHYGITPDLSTFGKIIGGGMPVGAYGGRRELMEQIA 286

Query: 291 PGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGD 347
           P G     GT +GNP+A  A L +L++ ++     +     + L DGL A+A+       
Sbjct: 287 PAGPIYQAGTLSGNPVAMAAGLAMLELIQEAGFYDRLAARTRLLADGLQAVADGEGVPFS 346

Query: 348 VRGLGAMIAI 357
              +GAM  +
Sbjct: 347 TNRVGAMFGL 356


Lambda     K      H
   0.320    0.137    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: 446
Number of extensions: 22
Number of successful extensions: 5
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: 426
Length of database: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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 (21.8 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:

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