GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Desulfatiglans anilini DSM 4660

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_035253180.1 H567_RS0101805 aspartate aminotransferase family protein

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000422285.1:WP_035253180.1
          Length = 407

 Score =  242 bits (618), Expect = 1e-68
 Identities = 141/372 (37%), Positives = 210/372 (56%), Gaps = 20/372 (5%)

Query: 10  LVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDERE 69
           LVRGEG  VWDE G+ YLD + GI V  LGH+ P     +  Q  K+V    ++    + 
Sbjct: 32  LVRGEGCRVWDEAGKSYLDFVGGIAVCALGHSSPLVTRILEEQSRKLVHVSNLYYTQPQA 91

Query: 70  EMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR------LATGRSEIVAMTNAFHGRTLG 123
           E+   L      +  +  NSG EA EAAIK AR          R  IV+M N+FHGRT+ 
Sbjct: 92  ELARLLVEHSFADRCFFCNSGAEANEAAIKLARRWAHEKYGPERYHIVSMANSFHGRTMA 151

Query: 124 SLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEE 183
           +LSAT + K ++G+ PL+ GFK +PFN++EA  +A+     AVI EPIQGEGG+V     
Sbjct: 152 TLSATGQAKIQKGYDPLLQGFKFVPFNDLEALSQAVDGTVCAVILEPIQGEGGVVVPSPG 211

Query: 184 FVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL 242
           +++ +R L ++ G LLI DEVQ G+ RTG+  A EH+GV PDI+++ K + NG P+   L
Sbjct: 212 YLEGVRRLCDERGTLLIYDEVQVGMGRTGRLFAHEHFGVAPDIMSLAKALANGLPMGAML 271

Query: 243 TDLEIP----RGKHGSTFGGNPLACRAVATTLRILRRDRLVE---KAGEKF---MEFSGE 292
               +      G H +TFGG PL        L  +  D  ++   +AG  F   +E   +
Sbjct: 272 AREALTPAFGPGSHATTFGGTPLVSAVARAVLTSILEDGWLDHCREAGGYFRSRLEALRD 331

Query: 293 R---VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEE 349
           R   V + RG GL++G+ L  P G  VKA  + G L+N   +R++R +PPLI++ + +++
Sbjct: 332 RYGFVKEVRGIGLIVGMELDVPGGPIVKACMDEGFLINCTQDRILRFVPPLIVKKEEIDQ 391

Query: 350 ARKEIEGVLNDI 361
             + ++ +L  +
Sbjct: 392 LVEALDRILGSV 403


Lambda     K      H
   0.320    0.140    0.410 

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: 17
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: 362
Length of database: 407
Length adjustment: 30
Effective length of query: 332
Effective length of database: 377
Effective search space:   125164
Effective search space used:   125164
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 Jul 25 2024. The underlying query database was built on Jul 25 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