GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Desulfoscipio geothermicus DSM 3669

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase

Query= reanno::Putida:PP_4108
         (416 letters)



>NCBI__GCF_900115975.1:WP_207545101.1
          Length = 434

 Score =  326 bits (835), Expect = 9e-94
 Identities = 180/429 (41%), Positives = 258/429 (60%), Gaps = 29/429 (6%)

Query: 6   ISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT 65
           I++ I+    + +   + A + D +GK YIDF GGIG LN GHC   VVEAI+ QA +L 
Sbjct: 16  IARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVVEAIKNQAEKLL 75

Query: 66  HYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAF 125
           H  F    + PYL L E+L +  P ++    M  NSGAE  ENA+K+AR    +  II+F
Sbjct: 76  HTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIARSYAKRTGIISF 135

Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLP------------YPSADTGVTCEQ 173
           +  FHGRTL T++L  KV PYK   G     VY +P            YP  + G+ C  
Sbjct: 136 ECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTYRSTYP--ECGLHC-- 191

Query: 174 ALKAMDRLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQ 233
            L+  DR+F+ E+  E++AA I EPVQGEGGF+   P F   LR+ CD+ GI++I DE+Q
Sbjct: 192 -LEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKHGIILIADEVQ 250

Query: 234 SGFGRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNP 293
           +GFGRTG+ FA    G+EPDL+ +AKSIA GMPL AVVG+ ++M A   G +GGTYSGNP
Sbjct: 251 TGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEIGGTYSGNP 310

Query: 294 ISCAAALASLAQMTDENLA----TWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRG 349
           +SCAA LA++  M  +NL       G++ +Q +++  E++      P IG + G+GAM  
Sbjct: 311 VSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKY------PIIGDVRGLGAMNA 364

Query: 350 IEFANADGS--PAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDI 407
           +E      +  PA  + A V++     G++++ +G   +++R L PL I  E LE+GLD+
Sbjct: 365 MELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLDV 424

Query: 408 LEQCLAELN 416
           LEQ +A ++
Sbjct: 425 LEQAVASVS 433


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: 461
Number of extensions: 18
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: 434
Length adjustment: 32
Effective length of query: 384
Effective length of database: 402
Effective search space:   154368
Effective search space used:   154368
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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