GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Cupriavidus basilensis 4G11

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 RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__Cup4G11:RR42_RS21370
          Length = 420

 Score =  576 bits (1485), Expect = e-169
 Identities = 287/420 (68%), Positives = 335/420 (79%), Gaps = 1/420 (0%)

Query: 1   MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60
           M N E  +R+ +ATPRGVGVMCNFFA+ AEN+ + DVEG  YIDFAAGIAVLNTGHRHP 
Sbjct: 1   MKNAELVRRKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPR 60

Query: 61  LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120
           LV A+++QL++FTHTAYQIVPY SY+ LAE+IN  AP  G  KTAFFTTGAEAVENA+KI
Sbjct: 61  LVEAMQRQLERFTHTAYQIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKI 120

Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180
           ARA TGRPGVIAFSGGFHGRT M MALTGKV PYK+GFGPFPG V+H PYP  LHG+S +
Sbjct: 121 ARAATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVE 180

Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240
           D+L A+E LFK+D++ K+VAAIIFEPVQGEGGFNVAP   V A+R +CDEHGI+++ADEV
Sbjct: 181 DALKAMEHLFKADVDPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEV 240

Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300
           Q+GF RTGKLFAM+HY   PDL TMAKSLAGGMPLS V G A +MDAPAPGGLGGTYAGN
Sbjct: 241 QTGFGRTGKLFAMEHYDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGN 300

Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360
           PLAVA+A AVL++++ E L  R   LGQRL   L   K  VP IA +RGLG+M+AVEF  
Sbjct: 301 PLAVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEFRR 360

Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420
              G P A   +++Q RAL QGLLLL+CG YGNVIRFL+PLTI DA  +  + IL D L+
Sbjct: 361 AD-GAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILADVLT 419


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: 606
Number of extensions: 16
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: 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 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