GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Brucella inopinata BO1

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_000182725.1:WP_008507916.1
          Length = 403

 Score =  324 bits (830), Expect = 3e-93
 Identities = 175/384 (45%), Positives = 234/384 (60%), Gaps = 5/384 (1%)

Query: 21  YAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNV 80
           Y  AA    RGEG  +  + G   IDFA GIAV SLGH+HP LV+ L  QA+++WH+SN+
Sbjct: 14  YNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEKLWHLSNI 73

Query: 81  FTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNS 140
           +      +L R+LV+ TFA++VF  NSGAEA E A K ARRY      P+++ II    +
Sbjct: 74  YEIPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGHPERFRIITFEGA 133

Query: 141 FHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQGEGG 200
           FHGRTL T+  GGQ KY +GFGPK EG   VP+ D  AL+AAI+ +T  ++LEPIQGEGG
Sbjct: 134 FHGRTLATIAAGGQAKYLEGFGPKVEGFDQVPFGDEAALRAAITPETAGILLEPIQGEGG 193

Query: 201 VLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGG 260
           +    + +L   R++CDE+  LL+ DEVQ+G+GR G+ FA+   G+ PDI++ AK +GGG
Sbjct: 194 LRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRTGKFFAHEWAGIRPDIMAIAKGIGGG 253

Query: 261 FPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKS 320
           FPIGA L T E AK ++ G HGTTYGGNPL  AV  A LDV+     ++ V+A     K 
Sbjct: 254 FPIGACLATAEAAKGMTAGMHGTTYGGNPLGMAVGNAVLDVVLADGFMENVQATALVMKQ 313

Query: 321 RLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVRFA 379
            L  +   Y  +  EIRG GLL+G             ++ A   E V+ + A  +VVR  
Sbjct: 314 GLASLVDRYPNVVSEIRGRGLLMGLKCV----VPNTSLIQALRDEHVLSVGAGDNVVRLL 369

Query: 380 PSLVIDDAEIDEGLERFERAVAKL 403
           P L+    E  E L+  E AV +L
Sbjct: 370 PPLITTPEEAREALKHIETAVERL 393


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: 453
Number of extensions: 23
Number of successful extensions: 2
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: 403
Length adjustment: 31
Effective length of query: 375
Effective length of database: 372
Effective search space:   139500
Effective search space used:   139500
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.

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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