GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pontibacter ramchanderi LP43

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_101444294.1 BD749_RS10520 ornithine--oxo-acid transaminase

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_002846395.1:WP_101444294.1
          Length = 413

 Score =  245 bits (626), Expect = 2e-69
 Identities = 143/395 (36%), Positives = 213/395 (53%), Gaps = 9/395 (2%)

Query: 14  DRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQR 73
           ++Y   NY P   +  +GEG  +WD  G+   DF    +  + GH HP ++ AL EQAQ+
Sbjct: 17  EKYGAHNYHPLPVVLSKGEGVYLWDVEGKRYYDFLSAYSAVNQGHCHPRIINALIEQAQQ 76

Query: 74  IWHVSNVFTNEPALRLARKLVDATFA-ERVFLANSGAEANEAAFKLARR--YANDVYGPQ 130
           +   S  F N+  L +A K +   F  ++    NSGAEA E A KLAR+  Y      P 
Sbjct: 77  LTLTSRAFYNDK-LGIAEKYICELFGYDKSLYMNSGAEAVETAIKLARKWGYLKKGIAPH 135

Query: 131 KYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK--TC 188
             EII    +FHGRT   ++    P  + GFGP   G   +PYNDLEAL+ A+ +    C
Sbjct: 136 NAEIIVVERNFHGRTTGIISFSTDPDSTKGFGPYMPGFKVIPYNDLEALETALKENPNVC 195

Query: 189 AVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVP 248
             ++EPIQGE GV+  Q  YL  A  LC E+N LL+ DE+Q+G+ R G++ A  +  V  
Sbjct: 196 GFLVEPIQGEAGVVVPQDGYLAKAHALCKEYNVLLMADEIQTGIARTGKMLASYYDDVKA 255

Query: 249 DILSSAKSLGGG-FPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEV 307
           DIL   K+L GG  P+  +L   +I   +  G HG+T+GGNP+A+AVA AAL+VI    +
Sbjct: 256 DILILGKALSGGVLPVSCVLANDDIMLCIQPGEHGSTFGGNPMAAAVAIAALEVIKEENL 315

Query: 308 LDGVKAKHERFKSRLQKI-GQEYGIFDEIRGMGLLIGAALTDEWKGK-ARDVLNAAEKEA 365
           ++      E F+ R+ ++  +   +   +RG GLL    +     G+ A DV    ++  
Sbjct: 316 VENAYKLGEIFRDRMNQLKAKRPEVVTLVRGRGLLNAIVIEPAADGRTAWDVCVELKENG 375

Query: 366 VMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAV 400
           ++      D++RFAP LV+ + ++ E  +  ER V
Sbjct: 376 LLAKPTHGDIIRFAPPLVMTEEQLHECCDIIERVV 410


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: 418
Number of extensions: 22
Number of successful extensions: 6
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: 413
Length adjustment: 31
Effective length of query: 375
Effective length of database: 382
Effective search space:   143250
Effective search space used:   143250
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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