GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Desulfoscipio geothermicus DSM 3669

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_900115975.1:WP_092481894.1
          Length = 453

 Score =  204 bits (519), Expect = 4e-57
 Identities = 147/397 (37%), Positives = 210/397 (52%), Gaps = 29/397 (7%)

Query: 34  ATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFT-HTAYQIVPYQGYVTLAE 92
           +T  D+ G+ + D   G  + N GHRHP+V++A+  QL+R   H+   + P + +  LA+
Sbjct: 69  STFTDIWGKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQRQALHSQELLDPLRAF--LAK 126

Query: 93  RINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPGVIAFSGAFHGRTLLGMALTGK 152
            + ++ P   L       +G E+VE  IK A+ +TGR   I+ + AFHG++L  ++ T K
Sbjct: 127 LLGSITP-GDLQYAFFVNSGTESVEAGIKFAKMYTGRRSFISTTRAFHGKSLGSLSATAK 185

Query: 153 VAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVAAIIVEPVQGE 212
              ++  F P     +H P+ +A      E     LE       D   VAA+IVEPVQGE
Sbjct: 186 -GVFRKPFLPLIPGFHHVPYGNA------EAVEMMLESCAFVGED---VAAVIVEPVQGE 235

Query: 213 GGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEPDLITMAKSLA 272
           GG    P D++  LR +CD++G +LI DEVQTG GRTGKMFA  H +V PD++ +AK+  
Sbjct: 236 GGVIIPPEDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHSNVVPDILCLAKAFG 295

Query: 273 GG-MPLSAVSGRAAIMDAPL--PGGLGGTYAGNPLAVAAAHAVIDVIEEEKLCERSASLG 329
           GG MP+ A   R  + +  +  P     T+ GNP+  AAA A I+V+ EE L +RSA  G
Sbjct: 296 GGIMPIGATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINVLLEENLPQRSAESG 355

Query: 330 QQLREHLLAQRKHCPAMA-EVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALEAGLVLL 388
             +   L    +  PA+  EVRG G M+  EF +   G    E AK +  R       +L
Sbjct: 356 VYMLGKLRELAEKYPAVVQEVRGKGLMIGIEFFNDELGY---EVAKGLFARG------VL 406

Query: 389 TCGTYGNV--IRFLYPLTIPQAQFDAALAVLTQALAE 423
             GT  N   IR   PLTI + Q D  +  L   LAE
Sbjct: 407 VAGTLINAKSIRIEPPLTISREQQDQVIERLDNTLAE 443


Lambda     K      H
   0.321    0.136    0.400 

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: 448
Number of extensions: 24
Number of successful extensions: 5
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: 423
Length of database: 453
Length adjustment: 32
Effective length of query: 391
Effective length of database: 421
Effective search space:   164611
Effective search space used:   164611
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 (21.9 bits)
S2: 51 (24.3 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