GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Methanospirillum lacunae Ki8-1

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>NCBI__GCF_003173355.1:WP_109969613.1
          Length = 384

 Score =  215 bits (548), Expect = 2e-60
 Identities = 147/407 (36%), Positives = 212/407 (52%), Gaps = 54/407 (13%)

Query: 26  IFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAYE 85
           I +      TV D +G++ +D   GIAV +TGH HPKVV A+ EQ  ++ H C  +    
Sbjct: 23  IMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIH-CSNLFYVP 81

Query: 86  PYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGGYHGRTMM 145
               L +K+ ++     + K     +G+EA+E A+K+AR  TGR   IA  GG+HGRTM 
Sbjct: 82  HQGALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLARIRTGRKEFIACEGGFHGRTMG 141

Query: 146 TLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDAEPRDIAAII 205
           +L  T K       M L P   F +  P              V+ +    A   + AA+I
Sbjct: 142 SLACTHKPAIREPFMPLQP---FTSFVP-----------YGDVQAL--KGAITEETAAVI 185

Query: 206 LEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLT 265
           LEP+QGEGG +  P   +K++R +CD  G+LLI DEVQ+G GRTG +FA ++ G+ PD+ 
Sbjct: 186 LEPIQGEGGVIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEGIHPDII 245

Query: 266 TFAKSIAGGFPLAGVC-------GKAEYMDAIAPGGLGGTYAGSPIACAAALAVIEVFEE 318
           T AK++A GFP+  +        GK+E+         G T+AG PIACAAALA I+V   
Sbjct: 246 TMAKAMASGFPMGAIVAREGLEFGKSEH---------GSTFAGGPIACAAALASIDVI-- 294

Query: 319 EKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVVA 378
            K+L    A GER  A L  +  +      V+GL  MI + +   G H  +       V 
Sbjct: 295 GKVLPEVAAKGERFRAALAHLNPR------VKGL--MIGITI---GDHCAD-------VQ 336

Query: 379 KAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEIA 425
           K      +L++C  +GN LR++ PLT  +A +DK   II    ++ A
Sbjct: 337 KECAVHGLLVNCAAHGN-LRLVPPLTITNAEIDKATGIINAAVSKFA 382


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: 458
Number of extensions: 31
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: 425
Length of database: 384
Length adjustment: 31
Effective length of query: 394
Effective length of database: 353
Effective search space:   139082
Effective search space used:   139082
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