GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Dechlorosoma suillum PS

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase

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



>FitnessBrowser__PS:Dsui_3250
          Length = 390

 Score =  187 bits (474), Expect = 6e-52
 Identities = 143/410 (34%), Positives = 202/410 (49%), Gaps = 45/410 (10%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           P+  SHG    ++DTDGK Y+D + GI V  LGH +P +V AI +QA R+ H +     +
Sbjct: 12  PVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVLHTS-----N 66

Query: 75  GPYLALMEQLS-QFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRA-----IIAFDGG 128
              + L E+L+ +   +S        NSG EA E A+K+AR    ++      II  +  
Sbjct: 67  LYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQKGVDAPVIIVMEKA 126

Query: 129 FHGRTLATLNLNGKVAPYKQRVGELP--GPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186
           FHGRTLATL+  G     K + G  P       +PY   D       A++A   L     
Sbjct: 127 FHGRTLATLSATGN---RKAQAGFEPLVSGFVRVPYNDLD-------AIRAAAELNP--- 173

Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246
              +V A + E VQGEGG    DP F + LR  CDE+  L++ DE+Q G GRTG  F F 
Sbjct: 174 ---NVVAVLLEMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQ 230

Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306
             GI PD+  LAK +  G+P+GA +   +       G  G T+ GNP++CAAAL ++A +
Sbjct: 231 HAGILPDVATLAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACI 290

Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIG--RLTGVGAMRGIEFANADGSPAPAQL 364
            +E L      Q +AI     R  +  L+   G   + G G M GIE       P    +
Sbjct: 291 EEEKLRENAVAQGEAI----RRGLSEALAGVGGLVEIRGKGLMLGIEL----DRPCGELV 342

Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
           AK +EA    GLL+  +  A  ++RLL  LT  A   +E +  L   + E
Sbjct: 343 AKGLEA----GLLI--NVTAEKVVRLLPALTFSAADTQELVQRLAALIKE 386


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: 408
Number of extensions: 21
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: 390
Length adjustment: 31
Effective length of query: 385
Effective length of database: 359
Effective search space:   138215
Effective search space used:   138215
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 Sep 17 2021. The underlying query database was built on Sep 17 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