GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Thiomicrospira cyclica ALM1

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013835162.1 THICY_RS03115 diaminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::Q88FI7
         (416 letters)



>NCBI__GCF_000214825.1:WP_013835162.1
          Length = 428

 Score =  156 bits (394), Expect = 1e-42
 Identities = 122/403 (30%), Positives = 192/403 (47%), Gaps = 17/403 (4%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAI--QAQATRLTHYAFNA- 71
           P       +A + D +GKRYIDF GG G LN GH +P + +A+    Q   +T+    A 
Sbjct: 21  PAVFDTATSATIVDVEGKRYIDFFGGAGSLNYGHNHPLINQALITYIQRNGITNALDKAT 80

Query: 72  -APHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFH 130
            A H    A    + +   + Y +   +  +GA   E ALK+AR    +  +IAF   +H
Sbjct: 81  VAKHDFISAFQSIILKPRKMDYKIQ-FVGPTGANGVETALKLARKMKKRSNVIAFTNAYH 139

Query: 131 GRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSA-DTGVTCEQALKAMDRLFSVELAVE 189
           G +L  L + G    Y     ++P  V  +PY +  D  +     L+    L       E
Sbjct: 140 GHSLGALAVTGNEF-YHGDYYDVPRNVNKMPYDNYFDHDMDSVDMLRHY--LGDGSSGYE 196

Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249
             AA I E +QGEGG       + Q L   C E  IL+I+DEIQ G GRTG  F+F R G
Sbjct: 197 LPAAVIVESIQGEGGINVASVGWLQKLSALCKEMDILLIMDEIQVGNGRTGDYFSFERAG 256

Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDE 309
           I PD++ L+KSI  GMP+  V+ +  +    P G   GT+ GN  +  A  A+L    ++
Sbjct: 257 IMPDIITLSKSIGTGMPMSIVLMKPSVDVWSP-GEHTGTFRGNSYAFIAGAAALELWRND 315

Query: 310 NLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369
           + +     + + + + ++ ++A     +I  + G+G + G+E      S       +V +
Sbjct: 316 DFSRSIRAKGKQVEAAFKDFQAR-FPGWITDVRGLGMIWGLE------SLVEGFCNEVSK 368

Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
            A  RGL++  +G +  +++ L PL I    L EG +IL   +
Sbjct: 369 QAFQRGLMMETAGASDQVLKFLGPLVISETELNEGFEILTDAI 411


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: 391
Number of extensions: 19
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: 428
Length adjustment: 32
Effective length of query: 384
Effective length of database: 396
Effective search space:   152064
Effective search space used:   152064
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