GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Escherichia coli BW25113

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__Keio:16484
          Length = 412

 Score =  451 bits (1159), Expect = e-131
 Identities = 221/389 (56%), Positives = 283/389 (72%), Gaps = 5/389 (1%)

Query: 4   EWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPN 63
           E  F ++ +LP YVF +  ELK   RR GEDI+D  MGNPD     HI++KLC VA RP+
Sbjct: 7   ERRFTRIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQRPD 66

Query: 64  VHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVI 123
            HGYS S+GIPRLR+AI  +Y+ RY VE+DPE  AI+TIG+KEG +HLMLA L+ GDTV+
Sbjct: 67  THGYSTSRGIPRLRRAISRWYQDRYDVEIDPESEAIVTIGSKEGLAHLMLATLDHGDTVL 126

Query: 124 VPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHN 183
           VPNP+YPIH Y  +I G    SVP++   DF       L   I+ S+ KPK ++L FP N
Sbjct: 127 VPNPSYPIHIYGAVIAGAQVRSVPLVEGVDF----FNELERAIRESYPKPKMMILGFPSN 182

Query: 184 PTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSM 243
           PT  CV+LEFF++VV LAK+  + +VHD AYAD+ +DG+  PSI+QV GA DVAVE +++
Sbjct: 183 PTAQCVELEFFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPGARDVAVEFFTL 242

Query: 244 SKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREI 303
           SK ++MAGWR+ F+VGN+ L+  LA +KSY DYG FTP+QVA+I ALE   + V    E 
Sbjct: 243 SKSYNMAGWRIGFMVGNKTLVSALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQ 302

Query: 304 YRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEE-VGMNSLDFSLFLLREAKVAVSPGI 362
           Y+RRRDVLV+GL+  GW V+ PK SM+VWAK+PE    M SL+F+  LL EAKV VSPGI
Sbjct: 303 YKRRRDVLVKGLHEAGWMVEMPKASMYVWAKIPEPYAAMGSLEFAKKLLNEAKVCVSPGI 362

Query: 363 GFGEYGEGYVRFALVENEHRIRQAVRGIK 391
           GFG+YG+ +VRFAL+EN  RIRQA+RGIK
Sbjct: 363 GFGDYGDTHVRFALIENRDRIRQAIRGIK 391


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: 549
Number of extensions: 26
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: 412
Length adjustment: 31
Effective length of query: 371
Effective length of database: 381
Effective search space:   141351
Effective search space used:   141351
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