GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Herbaspirillum seropedicae SmR1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= BRENDA::P42588
         (459 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05420 HSERO_RS05420
           4-aminobutyrate aminotransferase
          Length = 426

 Score =  196 bits (498), Expect = 1e-54
 Identities = 134/379 (35%), Positives = 207/379 (54%), Gaps = 30/379 (7%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTL 133
           L D +G+ FID   G  + N GHR+P ++ A++ Q+ K   H+   + P  +   LA+ +
Sbjct: 38  LWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFT-HTAYQIVPYASYVELAERI 96

Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192
             LTPG   K + F ++G E+VE A+K+A+A+    G    IA +G FHG+++  ++ T 
Sbjct: 97  NRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPG---VIAFAGGFHGRTMMGMALTG 153

Query: 193 K-STFRKPFMPLLPGFRHVPFGN----------IEAMRTALNECKKTGDDVAAVILEPIQ 241
           K + ++  F P      H P+ +          +EA++  L +       VAA+ILEP+Q
Sbjct: 154 KVAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVK-GLFKSDIEAKRVAAIILEPVQ 212

Query: 242 GEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKA 301
           GEGG    P  ++  +R LCDE G L+I DEVQ+G GRTGK+FA EH +V PD++ +AK+
Sbjct: 213 GEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKS 272

Query: 302 LGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361
           L GG MP+ A     E+       P     T+ GNPLA A+ALA ++V+ E+ L  + ++
Sbjct: 273 LAGG-MPLSAVNGRAEIMDA--PAPGGLGGTYAGNPLAIASALAVLDVMEEEQLVTRGQR 329

Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFA--SEMFRQRVLVAGTL 419
            GD L +  ++L    P  + E RG G ++A+EF D   G   A  ++  +Q  L  G L
Sbjct: 330 LGDKLQEHLKELRSSVPQ-IAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALNNGLL 388

Query: 420 -----NNAKTIRIEPPLTL 433
                +    IR   PLT+
Sbjct: 389 LLTCGSYGNVIRFLFPLTI 407


Lambda     K      H
   0.320    0.135    0.393 

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: 443
Number of extensions: 24
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: 459
Length of database: 426
Length adjustment: 32
Effective length of query: 427
Effective length of database: 394
Effective search space:   168238
Effective search space used:   168238
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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