GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Escherichia coli BW25113

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Keio:16484
          Length = 412

 Score =  153 bits (386), Expect = 1e-41
 Identities = 104/353 (29%), Positives = 167/353 (47%), Gaps = 9/353 (2%)

Query: 28  EDVISLTIGQPDFFTPHH-VKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNY 86
           ED+I  ++G PD  TP H V+     A   +   Y+ + G   LR+A+  + + + D   
Sbjct: 36  EDIIDFSMGNPDGATPPHIVEKLCTVAQRPDTHGYSTSRGIPRLRRAISRWYQDRYDVEI 95

Query: 87  DAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPG--YEPIINLCGAKPVIVDTTS 144
           D ESE I+T G+ + +       L  GD V++P P YP   Y  +I     + V +    
Sbjct: 96  DPESEAIVTIGSKEGLAHLMLATLDHGDTVLVPNPSYPIHIYGAVIAGAQVRSVPLVEGV 155

Query: 145 HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204
             F    R I ++  P  K ++L +PSNPT   +  E  + + AL K  +V V+ D  Y+
Sbjct: 156 DFFNELERAIRESY-PKPKMMILGFPSNPTAQCVELEFFEKVVALAKRYDVLVVHDLAYA 214

Query: 205 ELTYD---RPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNV 261
           ++ YD    P        RD  +    LSKS++M GWRIGF+   K +   + ++  Y+ 
Sbjct: 215 DIVYDGWKAPSIMQVPGARDVAVEFFTLSKSYNMAGWRIGFMVGNKTLVSALARIKSYHD 274

Query: 262 SCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPSI 321
               +  Q AA+ A+         + EQYK+R D +   L   G  V  P  + Y++  I
Sbjct: 275 YGTFTPLQVAAIAALEGDQQCVRDIAEQYKRRRDVLVKGLHEAGWMVEMPKASMYVWAKI 334

Query: 322 KS--FGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGL 372
                 M S +F+  LL +A V + PG  F  YG+ +VR +   + D +R+ +
Sbjct: 335 PEPYAAMGSLEFAKKLLNEAKVCVSPGIGFGDYGDTHVRFALIENRDRIRQAI 387


Lambda     K      H
   0.319    0.135    0.388 

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: 344
Number of extensions: 13
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: 393
Length of database: 412
Length adjustment: 31
Effective length of query: 362
Effective length of database: 381
Effective search space:   137922
Effective search space used:   137922
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 (21.8 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