GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Sphingomonas koreensis DSMZ 15582

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Ga0059261_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__Korea:Ga0059261_1288
          Length = 401

 Score =  421 bits (1081), Expect = e-122
 Identities = 202/398 (50%), Positives = 277/398 (69%), Gaps = 7/398 (1%)

Query: 1   MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60
           MSEE  F ++K+LP YV A VN ++   R  GEDI+DLGMGNPD+PP QH+IDKLCEVA 
Sbjct: 1   MSEE--FYRIKRLPPYVIAEVNGMRAAARAAGEDIIDLGMGNPDLPPPQHVIDKLCEVAQ 58

Query: 61  RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120
           +P+ HGYS SKGIP LR+A  ++Y RR+GV++DPE   ++T+G+KEG + L  A+  PGD
Sbjct: 59  KPSAHGYSQSKGIPGLRRAQANYYGRRFGVDVDPESEVVVTMGSKEGLASLATAITAPGD 118

Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSF 180
            ++ PNP+YPIH +  II G    +VP  P+E + E   R +   +     +P  +V+++
Sbjct: 119 VILAPNPSYPIHTFGFIIAGATIRAVPTTPDEHYFESLERAMNFTVP----RPSILVVNY 174

Query: 181 PHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVEL 240
           P NPT   VDL F++ +V  AK+  +WI+ D AY++L +DG    SILQV+GA DVA+E 
Sbjct: 175 PSNPTAETVDLAFYERLVAWAKENKVWIISDLAYSELYYDGKPTVSILQVKGAKDVAIEF 234

Query: 241 YSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKN 300
            S+SK +SMAGWR+ F VGN+ LI  +  +KSYLDYG FTP+Q A+  AL  P ++VE N
Sbjct: 235 TSLSKTYSMAGWRIGFAVGNKQLIAAMTRVKSYLDYGAFTPVQAAACAALNGPQDIVEAN 294

Query: 301 REIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVS 359
           R++Y +RRDVLVE   R GW++  P  SMF WA +P  +  + SL+FS  LL  AKVAV+
Sbjct: 295 RQLYHKRRDVLVESFGRAGWDIPAPPASMFAWAPLPPALAHLGSLEFSKQLLSHAKVAVA 354

Query: 360 PGIGFGEYGEGYVRFALVENEHRIRQAVRGIKKALDKI 397
           PG+G+GE GEG+VR A+VENE R+RQA R ++K L  +
Sbjct: 355 PGVGYGENGEGFVRIAMVENEQRLRQAARNVRKYLQSM 392


Lambda     K      H
   0.322    0.141    0.425 

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: 506
Number of extensions: 25
Number of successful extensions: 3
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: 402
Length of database: 401
Length adjustment: 31
Effective length of query: 371
Effective length of database: 370
Effective search space:   137270
Effective search space used:   137270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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:

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