GapMind for Amino acid biosynthesis

 

Aligments for a candidate for OAT in Klebsiella michiganensis M5al

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= BRENDA::Q9FNK4
         (475 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26375 BWI76_RS26375 aspartate
           aminotransferase family protein
          Length = 421

 Score =  205 bits (521), Expect = 3e-57
 Identities = 137/405 (33%), Positives = 219/405 (54%), Gaps = 36/405 (8%)

Query: 64  RANGSTIWDPEGKRYIDFLAAYSAVNQGHCHPKIMKALQEQVEKLTLSSRAFYN-DKFPV 122
           +A  +T+WD EG   IDF A  + +N GH HPKI+ A+++Q++  T ++      + +  
Sbjct: 28  KAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQIVPYESYVT 87

Query: 123 FAERLTNMFGYD---MVLPMNTGAEGVETALKLARKWGHEKKNIPKDEAIIVSCCGCFHG 179
            AER+  +   D         TGAE VE A+K+AR +             +++  G FHG
Sbjct: 88  LAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAYTGRPG--------LITFGGGFHG 139

Query: 180 RTLAIVSMSCDNDATR-GFGPLLPGNLK----------VDFGDA-DSLEKIFKEK--GDR 225
           RT   ++++      + GFGP  PG++           +   DA  SL++IFK     D+
Sbjct: 140 RTFMTMALTGKVAPYKIGFGPF-PGSVYHAVYPNAAHGITTADAMKSLDRIFKADIAADQ 198

Query: 226 IAGFLFEPIQGEAGVIIPPDGYLKAVRELCTKYNVLMIADEVQSGLARSGKMLACDWEEI 285
           +A  + EPIQGE G  + P  +++A+R LC  + +L+IADEVQ+G AR+GK+ A    ++
Sbjct: 199 VAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDV 258

Query: 286 RPDMVILGKALGGGVIPVSAVLADKDVMLHIKPGQHGSTFGGNPLASAVAMASLDVIVEE 345
           +PD++ + K+L GG  P+S V+   +VM    PG  G T+ GNPLA A A A LDVI EE
Sbjct: 259 KPDLMTMAKSLAGG-FPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAVLDVIEEE 317

Query: 346 KLVERSASLGEELRIQLNEIKKQFPKYIKEVRGRGLFNAIEFNSESLSPVSAYDICLSLK 405
           +L +R+  LG  L+  LN+ ++  P  I +VRG+G   A+EFN       SA +I   ++
Sbjct: 318 QLCQRAERLGSHLKEVLNQARQSCPA-IADVRGQGSMVAVEFNDPQTGEPSA-EITRQIQ 375

Query: 406 ERG------VLAKPTHNTIVRLTPPLSISSDELRDGSEALHDVLE 444
           ++       +L+   +  ++R   PL+I   +     + L  VL+
Sbjct: 376 QKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVLK 420


Lambda     K      H
   0.318    0.136    0.400 

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: 447
Number of extensions: 25
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: 475
Length of database: 421
Length adjustment: 33
Effective length of query: 442
Effective length of database: 388
Effective search space:   171496
Effective search space used:   171496
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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