GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Thiomicrospira microaerophila ASL8-2

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_044410795.1 NA59_RS08125 aspartate aminotransferase family protein

Query= SwissProt::Q88FI7
         (416 letters)



>NCBI__GCF_000934765.1:WP_044410795.1
          Length = 392

 Score =  176 bits (446), Expect = 1e-48
 Identities = 123/376 (32%), Positives = 191/376 (50%), Gaps = 33/376 (8%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           PIT   G  A ++D  G+ Y+D V GI V +LGH +P +  A+  Q+ +L H +      
Sbjct: 13  PITFVEGEGATLYDEQGRAYLDAVSGIAVCSLGHAHPEIAHALCEQSKKLIHTS------ 66

Query: 75  GPYLALMEQL--SQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFD 126
             Y  + +QL   + + +S        NSGAEA E A+K+AR      G T    I+  +
Sbjct: 67  NLYHVVNQQLLADELIRLSGMDKVFFGNSGAEANEGAIKIARKYGNDQGKTNPE-ILVME 125

Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186
             FHGRT+ATL+  G      Q+V E     +H P  S    V  +       ++ S   
Sbjct: 126 NSFHGRTMATLSATGS-----QKVQE----GFH-PLVSGFVRVPFDDIAAVEQKIASHP- 174

Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246
              ++ A + EPVQGEGG       + +ALR  CD+  +L++IDEIQ+G GRTG+ FAF 
Sbjct: 175 ---NLVAILVEPVQGEGGVHVPKDGYLKALRALCDQHNLLLMIDEIQTGVGRTGKWFAFQ 231

Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306
              I PD+L LAK++  G+P+GA + R +    L  G  G T+ GNP++CAA LA +  +
Sbjct: 232 HEDILPDVLSLAKALGNGVPIGACLARGKAAEVLAPGNHGTTFGGNPLACAAGLAVIKTI 291

Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366
              N   +  +Q + ++S ++  + +G+   + ++ G G M GI+     G      L K
Sbjct: 292 EHHNFIDYVAKQGEIMISDFKA-RLAGIE-QVKQVRGKGYMIGIQLDRPCGELVKRALDK 349

Query: 367 --VMEAARARGLLLMP 380
             ++   R   + L+P
Sbjct: 350 NLLINVTRGDTIRLLP 365


Lambda     K      H
   0.320    0.137    0.402 

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: 385
Number of extensions: 13
Number of successful extensions: 4
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: 416
Length of database: 392
Length adjustment: 31
Effective length of query: 385
Effective length of database: 361
Effective search space:   138985
Effective search space used:   138985
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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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