GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Rhodobacter viridis JA737

Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate WP_110806203.1 C8J30_RS11905 aspartate aminotransferase family protein

Query= curated2:Q05174
         (450 letters)



>NCBI__GCF_003217355.1:WP_110806203.1
          Length = 393

 Score =  118 bits (296), Expect = 3e-31
 Identities = 110/409 (26%), Positives = 173/409 (42%), Gaps = 51/409 (12%)

Query: 43  GPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPY 102
           G WL     G+RYLDL +  A   LG         P  V  L   A       ++Y +P 
Sbjct: 21  GSWLWTE-DGSRYLDLGAGIAVNALGHAA------PELVATLTEQAGKLWHVSNLYRIPE 73

Query: 103 AKFVTTFARVLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLE 162
            + +     ++ +     +FF + G  A E A+K    +  +K G  +R+     +L   
Sbjct: 74  QERLADM--LVANTFADTVFFTNSGTEACELAVKMVRKYFYEK-GQPERS----DILTFS 126

Query: 163 RSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEAAE 222
            +FHGRS   ++   T+       P         P  +H      EA +           
Sbjct: 127 GAFHGRSSAAIAAAGTEKMVKGFGPLL-------PGFKHLPWGDLEAVK----------- 168

Query: 223 EAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGT 282
               A     A  L EPIQGEGG       FL+A++++C     L V DEVQ G   TG 
Sbjct: 169 ---AAVTDTTAAILIEPIQGEGGIRPAPEGFLKALREICDATGTLLVFDEVQCGVARTGR 225

Query: 283 AWAYQQLGLRPDLVAFGKKTQVCGVMGGGRIGEVESNVFAVSSRIS----STWGGNLADM 338
            +A++  G+ PD++   K     G+ GG  +G V +   A S   +    ST+GGN    
Sbjct: 226 LFAHEWAGVTPDVMMVAK-----GIGGGFPLGAVLATANAASGMTAGTHGSTYGGNPLGC 280

Query: 339 VRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAV--DLPDT 396
               +++E +     L+ V ++  +LR  LE L   HP +    RG+GLM  +   LP  
Sbjct: 281 AIGAKMIEIVTAPGFLEEVSRKAGFLRQRLEGLVAAHPDIFEEVRGQGLMLGLRCKLPPG 340

Query: 397 EQRDAVLRRMYTGHQVIALPCGTRGLRFRPPLTVTESELDQGLEALAAS 445
           +    V++  Y    ++ +P     LR  P LT+TE ++ + +  L A+
Sbjct: 341 D----VVKAAY-AQNLLTVPAADNVLRLLPALTITEDDMAEAVRRLEAA 384


Lambda     K      H
   0.321    0.136    0.411 

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: 394
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 450
Length of database: 393
Length adjustment: 32
Effective length of query: 418
Effective length of database: 361
Effective search space:   150898
Effective search space used:   150898
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