GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Rhodanobacter denitrificans FW104-10B01

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_021560695.1:WP_027489558.1
          Length = 408

 Score =  387 bits (995), Expect = e-112
 Identities = 201/395 (50%), Positives = 266/395 (67%), Gaps = 3/395 (0%)

Query: 15  RYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRI 74
           RY +P Y P   +   G+G+RVWD  GR+ +DF  GIAV +LGH  P L+ AL  QA ++
Sbjct: 14  RYWLPVYKPRELVLDHGKGARVWDTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQAHKL 73

Query: 75  WHVSNVFTNEPALRLARKLVDAT-FAERVFLANSGAEANEAAFKLARRYAN-DVYGPQKY 132
           WH SNVF  EP LRLA +LV A+ FAERVFL NSGAEANEAA KL R++A      P++ 
Sbjct: 74  WHSSNVFYTEPPLRLAEELVHASGFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERR 133

Query: 133 EIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAIS-DKTCAVV 191
            I+  + SFHGRTL TV    Q KY  G+ P  EG  ++ +ND EAL+A  +     AV+
Sbjct: 134 VIVTFNGSFHGRTLATVTATAQAKYQQGYEPLPEGFRYLDFNDAEALEATFAAGDVAAVM 193

Query: 192 LEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDIL 251
           LEP+QGEGGVLPA   +L+  R+LCD+H+ALLV DE+Q GMGR G LFA++H  VVPDI+
Sbjct: 194 LEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHDHVVPDIV 253

Query: 252 SSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGV 311
           + AK+LGGGFPIGAML   ++A+ +  G HGTT+GGNP+A+AVA  AL  +++P VL  V
Sbjct: 254 TLAKALGGGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALAKLSSPAVLMNV 313

Query: 312 KAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQA 371
           + +    ++ L +I  E  +F E+RG GL+IGA L D +KGKA  VL+ A    +++LQA
Sbjct: 314 ERQANDLRAGLARINHELQLFAEVRGRGLMIGAVLADAYKGKAGAVLDHAATRGLLLLQA 373

Query: 372 SPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVRG 406
            PDV+RF P L I D E+ +GL R   A++    G
Sbjct: 374 GPDVLRFVPPLTITDEELADGLARLHAALSDFAAG 408


Lambda     K      H
   0.318    0.135    0.394 

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: 470
Number of extensions: 18
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: 406
Length of database: 408
Length adjustment: 31
Effective length of query: 375
Effective length of database: 377
Effective search space:   141375
Effective search space used:   141375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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