GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Collimonas arenae Ter10

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_001584165.1:WP_128083232.1
          Length = 420

 Score =  555 bits (1429), Expect = e-162
 Identities = 275/413 (66%), Positives = 327/413 (79%)

Query: 7   HQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVE 66
           HQR+ +ATPRGVGVMC+F+A  A N+ + DVEG  +IDFAAGIAVLNTGHRHP LVAA++
Sbjct: 2   HQRKNAATPRGVGVMCDFYASHALNSEIWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQ 61

Query: 67  QQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTG 126
           +QL +FTHTAYQIVPY SYV LAE+INA+ P     KT FF+TGAEAVENAVKIARA TG
Sbjct: 62  EQLGKFTHTAYQIVPYGSYVELAERINAVTPGDHAKKTTFFSTGAEAVENAVKIARAATG 121

Query: 127 RPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAI 186
           R  VIAFSG FHGRT M MALTGKV PYK+GFGPFP  VYHVP+P +LHG+S ++SL A+
Sbjct: 122 RSAVIAFSGAFHGRTMMGMALTGKVVPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAAL 181

Query: 187 ERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFAR 246
           + LFK+D++ K+VAAII EPVQGEGGF  AP   + A+R+LCDEHGI+++ DEVQ+GFAR
Sbjct: 182 QSLFKADVDPKRVAAIILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFAR 241

Query: 247 TGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAA 306
           TGKLFA++H    PDLMTMAKSLAGGMPLS V G A IMDA APGGLGGTYAGNPLAVA+
Sbjct: 242 TGKLFAVEHSGVIPDLMTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVAS 301

Query: 307 AHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEP 366
           A AVL++I++E L ERAN LG RLK  L   +  VP IA +RGLG+M+AVEF  P + +P
Sbjct: 302 ALAVLDVIEEEKLVERANVLGGRLKQVLEGLRADVPQIADIRGLGAMVAVEFTQPGSKQP 361

Query: 367 SAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419
            A   +K+Q  AL  GLLLL+CG Y N IRFL+PLTI DA  D A+ IL  A+
Sbjct: 362 DADFTKKVQAEALKNGLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAM 414


Lambda     K      H
   0.319    0.134    0.388 

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: 597
Number of extensions: 27
Number of successful extensions: 1
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: 421
Length of database: 420
Length adjustment: 32
Effective length of query: 389
Effective length of database: 388
Effective search space:   150932
Effective search space used:   150932
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 Sep 24 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