GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Limnohabitans curvus MWH-C5

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_108401693.1 B9Z44_RS03080 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_003063475.1:WP_108401693.1
          Length = 398

 Score =  259 bits (661), Expect = 1e-73
 Identities = 151/364 (41%), Positives = 204/364 (56%), Gaps = 9/364 (2%)

Query: 31  GEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRLA 90
           G G RVWD +G+  +D   GIAV +LGHAHP L  AL +Q  ++ H  N +       LA
Sbjct: 24  GRGLRVWDTNGKAYLDALAGIAVNTLGHAHPQLTPALQDQVGKMIHSCNYYHIPLQEALA 83

Query: 91  RKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFTVN 150
            KLV+ +     F  NSG EANEAA KLAR++ + + G +K EI+    +FHGR+L T+ 
Sbjct: 84  AKLVELSGMTNAFFCNSGLEANEAAIKLARKFGH-MKGIEKPEIVVYEKAFHGRSLATLA 142

Query: 151 VGGQPKYSDGFGPKFEGITHVPYNDLEALKAAI--SDKTCAVVLEPIQGEGGVLPAQQAY 208
             G  K  +GFGP  EG   VP N++EALK A   +    AV  E IQGEGGV P    Y
Sbjct: 143 ATGNEKIKEGFGPMMEGYIRVPVNNIEALKKATEGNPNVAAVFFETIQGEGGVKPMNTDY 202

Query: 209 LEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAMLT 268
           L+  R+LCD+ + LL+ DEVQ GMGR G+ FA+   G+VPD++  AK LG G P+GA++ 
Sbjct: 203 LQQVRQLCDKRDWLLMIDEVQCGMGRTGKWFAHQWSGIVPDVMPLAKGLGSGVPVGAVVA 262

Query: 269 TGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKSRLQKIGQE 328
             + A     G HGTT+GGNPLA       + ++   ++LD V        + L +    
Sbjct: 263 GPKAAHIFQPGNHGTTFGGNPLAMRAGVETIRIMEEDKLLDNVLKVGAHLHAALHRELDG 322

Query: 329 YGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPD-VVRFAPSLVIDDA 387
                EIRG GL+IG  L      +   VL     +A ++L  + D VVR  P L+I +A
Sbjct: 323 VKGVKEIRGQGLMIGIDL-----DRPCGVLMQRALDAGLLLSVTADSVVRLVPPLIITEA 377

Query: 388 EIDE 391
           E DE
Sbjct: 378 EADE 381


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: 383
Number of extensions: 20
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: 406
Length of database: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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