GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04057 H281DRAFT_04057
           acetylornithine aminotransferase apoenzyme
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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