GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Amantichitinum ursilacus IGB-41

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_001294205.1:WP_053937056.1
          Length = 400

 Score =  236 bits (602), Expect = 9e-67
 Identities = 144/409 (35%), Positives = 227/409 (55%), Gaps = 40/409 (9%)

Query: 26  VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85
           +V  R   S VWD  G+EYIDF GGIAV + GH HP+++AA+ EQ  KL H    V   E
Sbjct: 21  IVPVRGAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHIS-NVFTNE 79

Query: 86  PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAAT------GRAGVIAFTGAY 139
           P + LA+ + +     F ++     SG+EA E A+K+AR A+       +  V++   ++
Sbjct: 80  PALALAKTLVEHT---FAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSF 136

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199
           HGRT  T+ + G+   YS G G  P GI             + + +AS+E +  +D    
Sbjct: 137 HGRTFFTVSVGGQP-KYSDGFGPKPAGIEHF----------KYNDLASLEALIDDDT--- 182

Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259
             A +IIEP+QGEGG    ++ F+Q +RALCD+   LLI DEVQ+G GRTG+ +A    G
Sbjct: 183 --ACVIIEPIQGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFG 240

Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319
           +VPD+ + AK +GGGFPI  +    ++   +  G  G TY G+P+A A A   + +    
Sbjct: 241 VVPDILSTAKGLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAVAGTAISIITRP 300

Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSK--- 376
           + L   +A  ER++AGL+ I  K+ V+ ++RG+G ++ ++L          AE   +   
Sbjct: 301 ETLSGVKAKSERIRAGLQAIADKYPVVAEIRGMGLLIGVQL---------KAEYAGRSRD 351

Query: 377 IVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425
           ++  A E+G+++L+ G   +V+RF   + I D +++ GLA + + F  L
Sbjct: 352 VLNAAAEEGVLVLAAGP--DVVRFAPSLVISDDEIDAGLARVEKAFARL 398


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: 419
Number of extensions: 22
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: 400
Length adjustment: 31
Effective length of query: 395
Effective length of database: 369
Effective search space:   145755
Effective search space used:   145755
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