GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Clostridium acetobutylicum ATCC 824

Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_010965684.1 CA_RS12260 aspartate aminotransferase family protein

Query= curated2:Q7SI94
         (388 letters)



>NCBI__GCF_000008765.1:WP_010965684.1
          Length = 387

 Score =  286 bits (731), Expect = 9e-82
 Identities = 154/378 (40%), Positives = 237/378 (62%), Gaps = 16/378 (4%)

Query: 4   LLKFYQDRGIKIIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEIST 63
           L+  Y    +   KGEG  ++D+  N+Y+D  +G  V  LGH N  I+  +++Q  ++  
Sbjct: 6   LMNTYGRFNVTFDKGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMH 65

Query: 64  LSLAFDTPIREEMIKELDEL--KPEDLDNLFLLNSGSEAVELALKIARKIT------KRR 115
           +S  +      E   EL E+  K  + D +F+ NSG+EA+E  LK+ARK         ++
Sbjct: 66  VSNYY----WNENAMELTEILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKK 121

Query: 116 KIVAFKNSFHGRSMGALSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKS-ITEDTAAVIV 174
           +I+   NSFHGR+MGALSVT   KY+E F+PLIG V+ +++N++D +K  I+  TAAVIV
Sbjct: 122 EIIYMDNSFHGRTMGALSVTGQPKYQESFKPLIGAVKSVKFNDLDDIKQKISSKTAAVIV 181

Query: 175 EPVQGEGGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILT 234
           EP+QGEGG+IPAKKE++K LR++ ++ NALLI DEVQ G GR G ++AYQ F++ PDI+ 
Sbjct: 182 EPIQGEGGIIPAKKEYLKLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKFEVVPDIVC 241

Query: 235 AGKAIGGGFPVSAVFLPNWISEKIEEGDHGSTYGGNPLAAAAVTAACKVAKSEKIAE--Q 292
             KA+GGGFP+ A+     ++     GDHG+TYGGNPLA A   A  K    +K+ E   
Sbjct: 242 IAKALGGGFPIGAMLAKESVASSFVPGDHGNTYGGNPLACAVAIAVLKELVDKKVVEINV 301

Query: 293 AQKKGELFMRILKEKLEDFKIVREIRGLGLMIGIDLKVNPSIAIKVLQDEKVLSLKAGLT 352
            +K   LF +++  K E +K++ ++RG+GL+IG+++  +    I    + K+L + AG  
Sbjct: 302 NEKSKYLFDKLMTLK-EKYKVINDVRGMGLLIGVEVACDVKKIINKCFESKLLLITAGKN 360

Query: 353 TIRFLPPYLITQSDMEWA 370
            +RFLPP  ++  +++ A
Sbjct: 361 VVRFLPPLNVSFEEIDKA 378


Lambda     K      H
   0.317    0.136    0.386 

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: 395
Number of extensions: 14
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: 388
Length of database: 387
Length adjustment: 30
Effective length of query: 358
Effective length of database: 357
Effective search space:   127806
Effective search space used:   127806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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