GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Paraburkholderia bryophila 376MFSha3.1

Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme

Query= curated2:Q05174
         (450 letters)



>FitnessBrowser__Burk376:H281DRAFT_04057
          Length = 394

 Score =  122 bits (307), Expect = 2e-32
 Identities = 121/409 (29%), Positives = 175/409 (42%), Gaps = 49/409 (11%)

Query: 43  GPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPY 102
           G WL D   G RYLD    +A   LG     +++    + + A    N   +P  Y  P 
Sbjct: 27  GSWLYDN-NGKRYLDFIQGWAVNCLGHCDEGMIEA---LNQQAKLLFNP--SPAFYNEPM 80

Query: 103 AKFVTTFARVLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLE 162
           AK      +         +FF + GA A E A+K A  W  +     D A    +++  +
Sbjct: 81  AKLAALLTQ---HSCFDKVFFANSGAEANEGAIKLARKWGKK---FKDGA---FEIITFD 131

Query: 163 RSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEAAE 222
            SFHGR+  TMS +           K  W  I AP +  P    A+ N  A    L  A+
Sbjct: 132 HSFHGRTLATMSASG----------KPGWDTIYAPQV--PGFPKADLNDIASVEKLINAK 179

Query: 223 EAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGT 282
                        + EPIQGEGG    + EF+Q +++L  +H+ L ++DEVQSGCG  GT
Sbjct: 180 TV---------AVMLEPIQGEGGVIPATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGT 230

Query: 283 AWAYQQLGLRPDLVAFGKKTQVCGVMGG----GRIGEVESNVFAVSSRISSTWGGNLADM 338
            +AY+  G+ PD++  GK     G+ GG      + + E  VF    +   T+ GN    
Sbjct: 231 LFAYELSGVEPDIMTLGK-----GIGGGVPLAALLAKAEVAVFEAGDQ-GGTYNGNPLMT 284

Query: 339 VRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDL-PDTE 397
                V+  +     L+ V  RG+YLR  L  L+E         RG GL+ A+ L  D  
Sbjct: 285 AVGYSVISQLTAPGFLEGVRARGEYLRAKLLELSEERG--FKGERGEGLLRALLLGKDIG 342

Query: 398 QRDAVLRRMYTGHQVIALPCGTRGLRFRPPLTVTESELDQGLEALAASL 446
            +     R      ++        LRF P L VT  E+DQ +  L + L
Sbjct: 343 NQIVEKARDMQPDGLLLNAARPNLLRFMPALNVTNEEIDQMMAMLRSIL 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: 345
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: 394
Length adjustment: 32
Effective length of query: 418
Effective length of database: 362
Effective search space:   151316
Effective search space used:   151316
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