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_092482996.1 BM299_RS08235 acetylornithine transaminase

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



>NCBI__GCF_900115975.1:WP_092482996.1
          Length = 396

 Score =  209 bits (533), Expect = 9e-59
 Identities = 136/403 (33%), Positives = 202/403 (50%), Gaps = 48/403 (11%)

Query: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA--FNAAPHGPYL 78
           G  A +WD DG+ ++DFVGGI V +LGHC+PAVV AIQ QA RL H +  +   P     
Sbjct: 28  GEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVSNLYYIEPQARLA 87

Query: 79  ALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGR 132
            L+ Q S    V +       NSGAEA E A+K+AR          K  II  +  FHGR
Sbjct: 88  ELLVQNSCCDRVFF------CNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGR 141

Query: 133 TLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVA 192
           TLA +   G+   Y+Q    LP    ++P+   D          A++R            
Sbjct: 142 TLAAITATGQ-PKYQQGFEPLPPGFKYVPFNDPD----------ALERAIGPH-----TC 185

Query: 193 AFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEP 252
           A + EPVQGEGG  A    +   +R  CD  G+L++ DE+Q G GRTG+  A+    +EP
Sbjct: 186 AVMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEP 245

Query: 253 DLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLA 312
           D++ LAK++ GG P+GA++ ++ + AA   G    T+ GNP++CAA LA++  M  +   
Sbjct: 246 DIITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGD--- 302

Query: 313 TWGERQEQAIVSRYERWKASGLS---PYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369
             G  Q    V  Y + K   L+    +I  + G+G + G+E     G         ++ 
Sbjct: 303 --GVMQNCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRPGGD--------IVN 352

Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
             R +GLL+  +    +++R   PL I  E ++  L+ +E  L
Sbjct: 353 RCREKGLLI--NCVNNNVLRFTPPLVIGTEEVDRALETVEAVL 393


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: 418
Number of extensions: 15
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: 396
Length adjustment: 31
Effective length of query: 385
Effective length of database: 365
Effective search space:   140525
Effective search space used:   140525
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 Apr 09 2024. 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