GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sinorhizobium fredii NGR234

Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate WP_010875176.1 NGR_RS30440 aspartate aminotransferase family protein

Query= SwissProt::Q84P54
         (515 letters)



>NCBI__GCF_000018545.1:WP_010875176.1
          Length = 467

 Score =  369 bits (946), Expect = e-106
 Identities = 183/423 (43%), Positives = 266/423 (62%), Gaps = 4/423 (0%)

Query: 83  DPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQLNTLPFYHSFWNR 142
           +P I+E  +G  + D +G + ID  AGL+C  +G     + +A ++Q   L +YHS+   
Sbjct: 33  EPTIVETGKGIRIQDARGNQLIDGFAGLYCVNVGYGRTEVAEAISRQAYRLAYYHSYAAH 92

Query: 143 TTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPNKKKFIARA 202
           TT     L+  L+ M   K M+K F+  SGS+AN+TQ KLVWYYNN  G+P KKK I+R 
Sbjct: 93  TTDELAILSDRLVKMAPGK-MSKVFYGMSGSDANETQAKLVWYYNNLRGKPTKKKIISRE 151

Query: 203 KAYHGSTLISASLTGLPALHQNFDLPAPFVLHTDCPHYWRYHLPGETEEEFSTRLAKNLE 262
           + YHG +++S S+TG+   H + DLP P + HT  PH++    PGETE EFS R A  L+
Sbjct: 152 RGYHGCSVVSGSMTGMSFYHDHMDLPLPQICHTGVPHHYWGANPGETEREFSARRAAELD 211

Query: 263 DLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILFIADEVICAFGRLG 322
           ++I   GP+ + AFIAEPV+G GG+ PPP  Y++ IQAV+KK+D+L IADEVI  FGR G
Sbjct: 212 EMIETLGPDNVGAFIAEPVLGTGGITPPPEGYWEAIQAVLKKHDVLLIADEVITGFGRTG 271

Query: 323 TMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNKLGSFSHGFTYSGH 382
           +MFGS  Y I+PDL+T+AK L+SAY P+ A +V  +V  V+   ++++G+FSHG+TYSGH
Sbjct: 272 SMFGSQHYGIEPDLITVAKGLTSAYFPLSASIVGEKVYKVLEDGADRVGAFSHGYTYSGH 331

Query: 383 PVACAVALEAIKIYKERNMVERVNRISPKFQEGLK-AFSDSPIIGEIRGLGLILATEFAN 441
           P+  A A   + I ++ ++      +   FQ  LK  F+  PI+GE+RG+GL+ A EF  
Sbjct: 332 PIGAAAANAVLDIVEKEDLPGNAREVGGYFQAQLKEKFAQLPIVGEVRGVGLMGAIEFVG 391

Query: 442 NKSPNDHFPPEWGVGAYFGAQCQKNGMLVRVA--GDTIMMSPPFVVTPEELDELIRIYGK 499
           ++     F P   VGA      +  G++ R    GD +  +PP V T EE+DE++ +  K
Sbjct: 392 DRENKKRFDPLLKVGARVSKAARDRGLIARAMPHGDILGFAPPLVTTKEEVDEIVAMAEK 451

Query: 500 ALR 502
           A+R
Sbjct: 452 AVR 454


Lambda     K      H
   0.318    0.135    0.402 

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: 613
Number of extensions: 29
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: 515
Length of database: 467
Length adjustment: 34
Effective length of query: 481
Effective length of database: 433
Effective search space:   208273
Effective search space used:   208273
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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