GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Shewanella sp. ANA-3

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= BRENDA::Q9I6M4
         (426 letters)



>lcl|FitnessBrowser__ANA3:7023380 Shewana3_0610 bifunctional
           N-succinyldiaminopimelate-
           aminotransferase/acetylornithine transaminase protein
           (RefSeq)
          Length = 405

 Score =  222 bits (565), Expect = 2e-62
 Identities = 150/397 (37%), Positives = 212/397 (53%), Gaps = 34/397 (8%)

Query: 26  VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85
           V+  R E S VWD EG E+IDFAGGIAV   GH HP ++ A++ Q  KL H    V+  E
Sbjct: 25  VIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLS-NVMTNE 83

Query: 86  PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-ATGRAGV-----IAFTGAY 139
           P +ELA    K V   F ++     SG+EA E A+K+AR  A  + GV     IAF  A+
Sbjct: 84  PALELA---TKLVNSTFAERVYFANSGAEANEAALKLARRYALEKFGVEKDEIIAFDKAF 140

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199
           HGRT  T+ + G+   YS G G  P  I               + +A++E      A   
Sbjct: 141 HGRTFFTVSVGGQAA-YSDGFGPKPQSITHL----------PYNDVAALEA-----AVSD 184

Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259
              AI++EP+QGEGG      +F++ +R L ++H  L+I DEVQTG GRTG  +A     
Sbjct: 185 KTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTD 244

Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319
           IVPD+ T AK++GGGFPI+ +   AEI + +  G  G TY G+P+ACA   AVL V    
Sbjct: 245 IVPDILTTAKALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTP 304

Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVV 379
           ++L   +   + L+ GL +I  K+ V  ++RG G ++   L E               +V
Sbjct: 305 EVLNGVKHREQLLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRS------RDFLV 358

Query: 380 RAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLA 416
            +  +GL+ L  G   NV+RF   + IP+A + +GLA
Sbjct: 359 ASVAEGLMSLMAGA--NVVRFAPSLVIPEADIAEGLA 393


Lambda     K      H
   0.319    0.137    0.393 

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: 416
Number of extensions: 20
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: 426
Length of database: 405
Length adjustment: 31
Effective length of query: 395
Effective length of database: 374
Effective search space:   147730
Effective search space used:   147730
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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