GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Desulfoscipio geothermicus DSM 3669

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase

Query= BRENDA::Q88RB9
         (425 letters)



>NCBI__GCF_900115975.1:WP_092481894.1
          Length = 453

 Score =  207 bits (527), Expect = 5e-58
 Identities = 140/398 (35%), Positives = 210/398 (52%), Gaps = 29/398 (7%)

Query: 34  STVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAYEPY-VELCE 92
           ST  D+ G+E ID  GG  + N GH HPKV+ AV +QL + +    ++L  +P    L +
Sbjct: 69  STFTDIWGKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQRQALHSQELL--DPLRAFLAK 126

Query: 93  KINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGGYHGRTMMTLGLTGK 152
            +  + PGD  +    V +G+E+VE  +K A+  TGR   I+ T  +HG+++ +L  T K
Sbjct: 127 LLGSITPGDL-QYAFFVNSGTESVEAGIKFAKMYTGRRSFISTTRAFHGKSLGSLSATAK 185

Query: 153 VVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDA-EPRDIAAIILEPVQG 211
            V     + L+PG           H +   +A A VE + ++ A    D+AA+I+EPVQG
Sbjct: 186 GVFRKPFLPLIPG----------FHHVPYGNAEA-VEMMLESCAFVGEDVAAVIVEPVQG 234

Query: 212 EGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSI 271
           EGG +  P++ + +LR LCD++G LLI DEVQTG GRTG  FA E   V PD+   AK+ 
Sbjct: 235 EGGVIIPPEDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHSNVVPDILCLAKAF 294

Query: 272 AGG-FPLAGVCGKAEYMDAIA--PGGLGGTYAGSPIACAAALAVIEVFEEEKLLDRSKAV 328
            GG  P+     +    + +   P     T+ G+P+ CAAA+A I V  EE L  RS   
Sbjct: 295 GGGIMPIGATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINVLLEENLPQRSAES 354

Query: 329 GERLTAGLREIQKKYP-IIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVVAKAR-EKGLI 386
           G  +   LRE+ +KYP ++ +VRG G MI +E F           +G  VAK    +G++
Sbjct: 355 GVYMLGKLRELAEKYPAVVQEVRGKGLMIGIEFFND--------ELGYEVAKGLFARGVL 406

Query: 387 LLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424
           +         +RI  PLT      D+ +  ++   AE+
Sbjct: 407 VAGTLINAKSIRIEPPLTISREQQDQVIERLDNTLAEV 444


Lambda     K      H
   0.320    0.138    0.395 

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: 503
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: 425
Length of database: 453
Length adjustment: 32
Effective length of query: 393
Effective length of database: 421
Effective search space:   165453
Effective search space used:   165453
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: 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