GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Lacinutrix algicola AKS293

Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78 (characterized)
to candidate WP_055435649.1 ASC41_RS05550 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::Q8KDS8
         (400 letters)



>NCBI__GCF_001418085.1:WP_055435649.1
          Length = 395

 Score =  363 bits (932), Expect = e-105
 Identities = 183/390 (46%), Positives = 260/390 (66%), Gaps = 1/390 (0%)

Query: 10  LSRRVLSMQESQTMKITGLAKKMQAEGKDVVSLSAGEPDFPTPENVCEAGIEAIRKGFTR 69
           LS R+ +M  S T+ +   A++++AEGKD++ LS GEPDF TP+ + EA I+A+   +  
Sbjct: 4   LSERITNMSTSATLAMAAKARELRAEGKDIIGLSLGEPDFNTPDFIKEAAIQAVNDNYNS 63

Query: 70  YTANSGIPELKKAIIRKLQRDNGLEYAEDEIIVSNGGKQALANTFLALCDEGDEVIVPAP 129
           Y+   G  +LK+A+I K +RDN L Y   +I+VS G KQ+L N    + ++GDEVI+P P
Sbjct: 64  YSPVDGYVDLKEAVITKFKRDNNLTYTLPQIVVSTGAKQSLYNIAQVMLNKGDEVILPCP 123

Query: 130 YWVSFPEMARLAEATPVIVETSIETGYKMTPEQLAAAITPKTRILVLNSPSNPSGAVYNE 189
           YWVS+ ++ ++AE  PV V+TSIE  +KMT  QL AAITPKT++L  +SP NPSG++Y++
Sbjct: 124 YWVSYSDIVKVAEGVPVEVKTSIENDFKMTASQLEAAITPKTKMLWFSSPCNPSGSLYSK 183

Query: 190 AEVRALMQV-IEGKEIFVLSDEMYDMICYGGVRPFSPARIPEMKPWVIVSNGTSKSYSMT 248
            E+ AL  V ++   I+V+SDE+Y+ I Y G    S A I  M    I  NG SK+++MT
Sbjct: 184 EELEALASVLVKYPNIYVVSDEIYEHINYTGKPHASMAGIDGMFNNTITVNGVSKAFAMT 243

Query: 249 GWRIGYLAAPKWIINACDKIQSQTTSNANSIAQKAAVAALDGDQSIVEQRRAEFEKRRDF 308
           GWR+G++ AP WI  AC+K+Q Q TS  N IAQ+A + AL+ D S+V+    EF+ RRD 
Sbjct: 244 GWRVGFIGAPDWIARACNKMQGQVTSGTNCIAQRAVITALNADPSVVDYMIDEFKVRRDM 303

Query: 309 MFRELNTISGIECTLPEGAFYIFPSIKGLLGKTFGGKVMKDSTDVAEYLLTEHYVATVPG 368
           +   L  I G +   PEGAFY+FP +    GKT  GK + ++TD + YLL E  VATV G
Sbjct: 304 VLNLLEGIEGFKTNTPEGAFYVFPDVTYFFGKTLRGKTINNATDFSLYLLEEALVATVTG 363

Query: 369 DAFGAPENLRLSYAASIEELAEAVNRIRKA 398
           DAFG P+ +R+SYAAS +++ EAV RI+ A
Sbjct: 364 DAFGNPDCIRISYAASQDQIKEAVKRIKAA 393


Lambda     K      H
   0.316    0.132    0.376 

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: 372
Number of extensions: 9
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
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 (21.6 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