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_092482996.1 BM299_RS08235 acetylornithine transaminase

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_900115975.1:WP_092482996.1
          Length = 396

 Score =  229 bits (583), Expect = 1e-64
 Identities = 141/392 (35%), Positives = 216/392 (55%), Gaps = 38/392 (9%)

Query: 30  RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89
           R E + +WD +GRE++DF GGIAV + GH HP V+ A+QEQ  +L H    +   EP   
Sbjct: 27  RGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVS-NLYYIEPQAR 85

Query: 90  LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIAFTGAYHGRT 143
           LAE + +    D   +     SG+EA E A+K+AR          +  +I    ++HGRT
Sbjct: 86  LAELLVQNSCCD---RVFFCNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGRT 142

Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203
           +  +  TG+   Y  G   +P G            V  +D  A +ER     A      A
Sbjct: 143 LAAITATGQP-KYQQGFEPLPPGF---------KYVPFNDPDA-LER-----AIGPHTCA 186

Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263
           +++EPVQGEGG Y  +  ++  +R LCD++G+LL+ DEVQ G GRTG F A +   + PD
Sbjct: 187 VMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEPD 246

Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323
           + T AK++GGGFPI  +  K  +  A APG    T+ G+P+ACAA LA ++    + +++
Sbjct: 247 IITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGDGVMQ 306

Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383
             +AVG   K  L+++  K+  I +VRGLG ++ +EL      ++P  ++V+    R RE
Sbjct: 307 NCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMEL------NRPGGDIVN----RCRE 356

Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415
           KGL L++C    NV+RF  P+ I   ++++ L
Sbjct: 357 KGL-LINC-VNNNVLRFTPPLVIGTEEVDRAL 386


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: 414
Number of extensions: 21
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: 426
Length of database: 396
Length adjustment: 31
Effective length of query: 395
Effective length of database: 365
Effective search space:   144175
Effective search space used:   144175
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 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