GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Cupriavidus basilensis 4G11

Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase

Query= curated2:Q05174
         (450 letters)



>FitnessBrowser__Cup4G11:RR42_RS16955
          Length = 395

 Score =  123 bits (308), Expect = 1e-32
 Identities = 125/410 (30%), Positives = 178/410 (43%), Gaps = 51/410 (12%)

Query: 43  GPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPY 102
           G WL D   G RYLD    +A   LG +   ++D  A V +  +  +  PS P  Y  P 
Sbjct: 27  GSWLTDH-NGKRYLDFVQGWAVNCLGHSNQAMID--ALVDQ--SKKLFNPS-PAFYNEPM 80

Query: 103 AKFVTTFARVLGDP-LLPHLFFVDGGALAVENALKAAFDW-KAQKLGLDDRAVNRLQVLH 160
            +     AR L D      +FF + GA A E A+K A  W +  K G         +++ 
Sbjct: 81  LRL----ARQLTDASCFDKVFFANSGAEANEGAIKLARKWGRKHKNGA-------FEIIT 129

Query: 161 LERSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEA 220
           ++ SFHGR+  TMS +           K  W  I AP +            +A+   L +
Sbjct: 130 MDHSFHGRTLATMSASG----------KAGWDTIFAPQVP--------GFPKADLNDLAS 171

Query: 221 AEEAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLT 280
            E+     D  +A  L EP+QGEGG    S EF+Q ++ L  +H  LF++DEVQ+GCG  
Sbjct: 172 VEKLIN--DKTVAIML-EPVQGEGGVIPASREFMQGLRKLADQHKLLFIVDEVQTGCGRC 228

Query: 281 GTAWAYQQLGLRPDLVAFGKKTQVCGVMGGGRIGEVESNVFAVSSRI---SSTWGGNLAD 337
           GT +AY+  G+ PD++  GK     G+ GG  +  +       S        T+ GN   
Sbjct: 229 GTMFAYELSGVEPDIMTLGK-----GIGGGVPLAALLCKAEVASFEAGDQGGTYNGNPVM 283

Query: 338 MVRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDLPDTE 397
               + V+  +     L SV  +G YLR+ L AL       +   RG GL+ A+ L    
Sbjct: 284 TAVGSAVISQLTAPGFLQSVQDKGAYLREQLLALTSEFG--LGGERGEGLLRALVLNKDI 341

Query: 398 QRDAVLRRMYTGHQVIALPCGTRG-LRFRPPLTVTESELDQGLEALAASL 446
               V        Q + L       LRF P L VT  E+DQ +  L   L
Sbjct: 342 GPQLVEEARDMQPQGLLLNSPRPNLLRFMPALNVTIEEIDQMISMLRTLL 391


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: 323
Number of extensions: 13
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: 450
Length of database: 395
Length adjustment: 32
Effective length of query: 418
Effective length of database: 363
Effective search space:   151734
Effective search space used:   151734
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 17 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