GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Desulfovibrio vulgaris Hildenborough

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate 207835 DVU2347 acetylornithine aminotransferase

Query= uniprot:Q5JFW3
         (362 letters)



>MicrobesOnline__882:207835
          Length = 399

 Score =  256 bits (655), Expect = 6e-73
 Identities = 145/375 (38%), Positives = 214/375 (57%), Gaps = 21/375 (5%)

Query: 5   RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64
           R  + + R EG  +WD +GR Y+DL++GI V  LGH HPE    M+RQ  K+V    +F 
Sbjct: 22  RYPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVSNLFY 81

Query: 65  HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGR------SEIVAMTNAFH 118
            +E+ ++ E+L   +     +  NSG EA EAAIK AR    R       E+V +T AFH
Sbjct: 82  QEEQLDLAEKLLSTLHCTKAFFCNSGAEANEAAIKLARRYMQRVRGVDAHEVVTLTGAFH 141

Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178
           GRTL +++AT ++++++GF P+  GF+   + +++A + AIT  TA V+ E +QGEGG+ 
Sbjct: 142 GRTLATVAATGQERFQDGFAPMPAGFRQAEWGDIDALRAAITPATAGVLVEMVQGEGGVR 201

Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237
           P  +++ + + DL  + G LL+ DE+Q+GL RTG+F A +HYGV PDIVT  K + NG P
Sbjct: 202 PMTQDYARAVADLCREKGVLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANGLP 261

Query: 238 VSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAG-------EKF 286
           +   +T  E+ +    G H +TFG   L     A TL I++RDRL E+A        E+F
Sbjct: 262 MGAMMTTDEVAQGFVAGSHATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMERF 321

Query: 287 MEFSGE---RVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIE 343
                +    + + RG GLMIGIVL        K L  RG + N    +V+RL+P L I+
Sbjct: 322 RAIGAKLPGTIEEVRGYGLMIGIVLTFSGKEVWKELVARGFVCNNTQEKVLRLVPALTID 381

Query: 344 GDTLEEARKEIEGVL 358
              L      +E +L
Sbjct: 382 EADLTAFADTLEDIL 396


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: 341
Number of extensions: 10
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: 399
Length adjustment: 30
Effective length of query: 332
Effective length of database: 369
Effective search space:   122508
Effective search space used:   122508
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