GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Shewanella halifaxensis HAW-EB4

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_012278671.1 SHAL_RS18655 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_000019185.1:WP_012278671.1
          Length = 405

 Score =  223 bits (568), Expect = 8e-63
 Identities = 143/397 (36%), Positives = 210/397 (52%), Gaps = 34/397 (8%)

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

Query: 86  PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-ATGRAG-----VIAFTGAY 139
           P +ELA    K V   F ++     SG+EA E A+K+ R  A  + G     +IAF  A+
Sbjct: 84  PALELA---TKLVEATFAERVYFANSGAEANEAALKLVRRYAMDKFGAEKDQIIAFDKAF 140

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199
           HGRT  T+ + G+   YS G G  P  I               + I ++E +F +     
Sbjct: 141 HGRTFFTVSVGGQAA-YSDGFGPKPQSITHV----------PFNDIEALEAVFSDKT--- 186

Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259
              A+++EP+QGEGG       F++ +RALCD+H  LL+ DEVQTG GR G  +A  +  
Sbjct: 187 --CAVMMEPLQGEGGIIDADPEFLKAVRALCDKHNALLVFDEVQTGVGRLGELYAYMRGD 244

Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319
           +VPD+ T AK++GGGFPI+ +    EI   +  G  G TY G+P+ACA   AV+ V    
Sbjct: 245 VVPDVLTTAKALGGGFPIAAMLTTKEIAAHLKIGTHGSTYGGNPLACAVGNAVMDVVNTP 304

Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVV 379
           ++L   +   +  + GL +I  K+ V  ++RG G ++      G   +        + +V
Sbjct: 305 EVLNGVKHREQLFRDGLNKINDKYDVFSEIRGQGLLI------GAVVNSKYQGRAKEFLV 358

Query: 380 RAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLA 416
               +G++ L  G   NV+RF   + IP+  + +GLA
Sbjct: 359 AGINEGVMSLVAGA--NVVRFTPSLVIPETDIAEGLA 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: 402
Number of extensions: 19
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: 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 24 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