GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Methylocystis bryophila S285

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_085771871.1 B1812_RS12405 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_002117405.1:WP_085771871.1
          Length = 398

 Score =  202 bits (513), Expect = 2e-56
 Identities = 140/390 (35%), Positives = 204/390 (52%), Gaps = 42/390 (10%)

Query: 41  GREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKR-VP 99
           G  Y+DF  G+AV + GH HP+++ A+Q+   +  H       Y+  I  AE +A+R V 
Sbjct: 29  GGRYLDFGAGVAVNSLGHAHPRLLEALQQGATRPWHVSN---LYQ--IPQAERLAQRLVD 83

Query: 100 GDFPKKTLLVTSGSEAVENAVKIAR---AATG---RAGVIAFTGAYHGRTMMTLGLTGKV 153
             F  +  L  SG+EA+E A+K AR   AA G   R  +I F GA+HGRT+ TL   G  
Sbjct: 84  ASFADEVFLCNSGAEAIECAIKTARKFHAANGEPQRYRLITFEGAFHGRTLATLSAGGNR 143

Query: 154 VPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEG 213
             Y  G G           P E    +    +A++E +   +      A ++IE +QGEG
Sbjct: 144 -KYLDGFG----------PPVEGFDQAPFGDLAAVETLIGPET-----AGVLIESIQGEG 187

Query: 214 GFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGG 273
           G  V    F++ LR LCDQ G+LL+ DEVQTG GR G+F A E+ G+ PD+   AK +GG
Sbjct: 188 GIRVFPLEFLRALRTLCDQRGLLLVVDEVQTGVGRLGSFLAIERAGVSPDIAALAKGLGG 247

Query: 274 GFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLK 333
           GFPI       E    +  G  G T+ G+P+A + A AVL V   E  LER + +   L+
Sbjct: 248 GFPIGACLATKEAAKGMTLGAHGSTFGGNPLAASIANAVLDVVLSEGFLERVKRLEPVLR 307

Query: 334 AGLREIQAKH-KVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRAREKGLILLSCG 392
             L E++ +H ++I  +RG G M  ++      T  P  E +      AR+ GL+L++ G
Sbjct: 308 QQLAELEDEHPQIIDSLRGEGLMFGLK------TRVPNLEFLK----AARDAGLLLVAAG 357

Query: 393 TYYNVIRFLMPVTIPDAQL-EKGLAILAEC 421
              NV+R L P+ I ++ + E G  + A C
Sbjct: 358 D--NVVRLLPPLIIDESHIAEAGKRLRAAC 385


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: 421
Number of extensions: 18
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: 398
Length adjustment: 31
Effective length of query: 395
Effective length of database: 367
Effective search space:   144965
Effective search space used:   144965
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 Apr 09 2024. 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