GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_174545208.1 HTA01S_RS19080 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_001592305.1:WP_174545208.1
          Length = 456

 Score =  233 bits (595), Expect = 7e-66
 Identities = 151/432 (34%), Positives = 230/432 (53%), Gaps = 20/432 (4%)

Query: 3   KTNESL-LKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHP 61
           K  E+L L  R  ++ RG G++ PVV +RA   T+ D +G  +ID + G+ V + G  HP
Sbjct: 26  KAQEALALSARTESMARGGGRM-PVVMDRAFGVTIKDPDGNTFIDLSAGVGVSSVGRCHP 84

Query: 62  KVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKK--TLLVTSGSEAVENA 119
           KV+ A+ +Q G L H     +      ELA +I++ +P        T    SGS+A+E A
Sbjct: 85  KVVEAIHQQSGVLMHA--MEVNSTKRTELAAKISEIMPEGLRGDCITFFAQSGSDALEAA 142

Query: 120 VKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCEL--- 176
           VK A+  TGR  +IAF G YHG    +  LT     Y  G G   GG+  A  P      
Sbjct: 143 VKFAKRVTGRHQIIAFHGGYHGVWNASNALTTGTA-YRKGYGPFMGGVIHAPYPYAYRFP 201

Query: 177 ----HGVSEDDSIASIERIFKND-AQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCD 231
               H  +E  +   ++ +         D+AA+I+EPVQGEGG+   S  F+Q LR  CD
Sbjct: 202 FDTTHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQLLRKACD 261

Query: 232 QHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIA 291
           + G LLI DEVQ GAGRTG  +A E  G+ PD+ TF K +GG  P++G+  ++++   I 
Sbjct: 262 KSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGMGGDVPMAGLVMRSDLAAKIP 321

Query: 292 PGGLGGTYAGSPIACAAALAVLKVFEEEK--LLERSQAVGERLKAGLREIQAKHKVIGDV 349
            G +  T+A + ++ A AL  + + ++ +  LL R+  +G   +  +R     +  +G+V
Sbjct: 322 DGSVPNTFAANSLSAAVALTNIGLLQDPELDLLNRAHQLGLEAQEYIRGF--NNPYVGEV 379

Query: 350 RGLGSMVAIELFEGGDTHKP-AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPD 408
           RG G M+ IEL E   T +P + E + K++      G++++ CG Y NV+R +  +TIP 
Sbjct: 380 RGRGLMIGIELVEDKATKEPLSGEKLGKLMGYVLSHGVLMVPCGRYTNVMRVMPSLTIPR 439

Query: 409 AQLEKGLAILAE 420
             L K L +  E
Sbjct: 440 KLLFKALDVFGE 451


Lambda     K      H
   0.319    0.137    0.393 

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: 485
Number of extensions: 28
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: 426
Length of database: 456
Length adjustment: 32
Effective length of query: 394
Effective length of database: 424
Effective search space:   167056
Effective search space used:   167056
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