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_053938113.1 WG78_RS12250 acetylornithine transaminase

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_001294205.1:WP_053938113.1
          Length = 405

 Score =  186 bits (471), Expect = 1e-51
 Identities = 136/399 (34%), Positives = 206/399 (51%), Gaps = 42/399 (10%)

Query: 29  ERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYI 88
           ER E + ++D  GR ++D+  G AV + GH  PK++A    Q      T        P  
Sbjct: 20  ERGEGAWLYDAAGRAWLDWLQGWAVNSLGHA-PKLVADTLYQQACTLITPSPAFNNTPAT 78

Query: 89  ELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-----ATGRAGVIAFTGAYHGRT 143
           +LA+ +      D   +  L  +G+EA E A+K+AR        G   +I FT A+HGRT
Sbjct: 79  QLAQWLVDHSCMD---QVFLANTGAEANEGAIKLARKWGRLHKDGAFEIITFTSAFHGRT 135

Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSED--DSIASIERIFKNDAQPQDI 201
           +  +  +GK           PG  +    P ++ G  +   + I S+ R+      P  +
Sbjct: 136 IAAMSASGK-----------PG--WDVYFPPQVPGFPKATLNDIESVRRLIG----PHTV 178

Query: 202 AAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIV 261
             I++EP+QGEGG    S++F+Q LRALCD+H +LLI DEVQTG GRTG  FA +  GI 
Sbjct: 179 G-IMLEPIQGEGGVNAASRAFLQALRALCDEHQLLLIFDEVQTGCGRTGPLFAYQASGIE 237

Query: 262 PDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKL 321
           PD+ T  K +G G PIS +  KA        G  GGT+ G+P+  A  LAV++   +   
Sbjct: 238 PDIMTLGKGLGAGVPISALLAKA-ACSVFEHGDQGGTFCGNPLTAAVGLAVMQHVAQPAF 296

Query: 322 LERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRA 381
           L    A G +L++GL E+ A+   +G+VRG G + AIEL   GD      E    ++  A
Sbjct: 297 LANVVARGAQLQSGLIELSARFG-LGEVRGAGLLWAIEL---GD------ERAEAVMRAA 346

Query: 382 REKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAE 420
           R+ GL++ +   +   +R +  +    A++E GLA+L +
Sbjct: 347 RDNGLLINNPRPH--CLRIMPALNTTAAEIETGLALLGK 383


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: 377
Number of extensions: 26
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 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