GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Shewanella oneidensis MR-1

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__MR1:199805
          Length = 405

 Score =  221 bits (562), Expect = 4e-62
 Identities = 150/397 (37%), Positives = 211/397 (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---TKLVNSTFAERVYFANSGAEANEAALKLARRYALEKHGVEKDEIIAFDKAF 140

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199
           HGRT  T+ + G+   YS G G  P  I               + +A++E      A   
Sbjct: 141 HGRTFFTVSVGGQAA-YSDGFGPKPQSITHL----------PFNDVAALEA-----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+ +    EI + +  G  G TY G+P+ACA   AVL V    
Sbjct: 245 IVPDILTTAKALGGGFPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTP 304

Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVV 379
           ++L   +   + L+ GL +I  K+ V  +VRG G ++   L E               +V
Sbjct: 305 EVLNGVKHREQLLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRS------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: 424
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 (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