GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Alicycliphilus denitrificans K601

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 WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000204645.1:WP_013518270.1
          Length = 398

 Score =  207 bits (526), Expect = 6e-58
 Identities = 134/410 (32%), Positives = 210/410 (51%), Gaps = 40/410 (9%)

Query: 7   LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAV 66
           L++  S  +    G++ PI  +R +  RVWDV G++YLD  GGIAV   GH HP++V A+
Sbjct: 4   LIEAASPHVMNTYGRV-PIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPAL 62

Query: 67  EAQLKKLSHTC--FQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124
           + Q+ KL HT   + V   E   EL  ++  +             TG EA E A+KIAR 
Sbjct: 63  QEQIAKLIHTSNYYHVPGQE---ELARLLTGRAR---MTNAFFCNTGLEANECAIKIARK 116

Query: 125 -----ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGIS 179
                  ++   + +  A+HGR+  T+  TG     +    L+ G +  A  P  +  + 
Sbjct: 117 YGVDKGIEKPEIVVYDHAFHGRSIATMTATGNPKVRNGFGPLLEGFIRVA--PNDIEALQ 174

Query: 180 EDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIAD 239
           E             +  P ++ A+++EP+QGEGG +     ++Q++R LCD +G +L+ D
Sbjct: 175 E-----------ATEGNP-NVVAVLMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLD 222

Query: 240 EVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYA 299
           EVQ+G GRTG  FA +  G+ PD+ T AK +  G P+  V       + + PG  G T+ 
Sbjct: 223 EVQAGMGRTGKWFAHQWAGIVPDVMTLAKGLGSGVPVGAVLAHGAASEVLKPGNHGSTFG 282

Query: 300 GNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIEL 359
           GNP+A  A +E +++ E+E LLQ A D+G  LK GL       P + +VRG G +I +EL
Sbjct: 283 GNPLAMRAGVETIRIMEEEGLLQNAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVEL 342

Query: 360 FEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQ 409
                 ++P       ++ RA   GL+L        V+R++  LT+  A+
Sbjct: 343 ------DRP----CGVLIDRAAQAGLLLSVTAD--RVIRLVPALTLTRAE 380


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: 444
Number of extensions: 21
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 395
Effective length of database: 367
Effective search space:   144965
Effective search space used:   144965
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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