GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ilvE in Marinobacter adhaerens HP15

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate GFF1728 HP15_1687 transcriptional regulator, GntR family with aminotransferase domain protein

Query= BRENDA::A0A060PQX5
         (417 letters)



>lcl|FitnessBrowser__Marino:GFF1728 HP15_1687 transcriptional
           regulator, GntR family with aminotransferase domain
           protein
          Length = 480

 Score =  161 bits (407), Expect = 4e-44
 Identities = 117/378 (30%), Positives = 183/378 (48%), Gaps = 12/378 (3%)

Query: 37  LLKLVESSDVISLAGGLPAPETFP--VEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLA 94
           LL +++ +    L   L A E  P  V +   I + +  +  A    Y    G   LR  
Sbjct: 109 LLDIMDRNAAFDLLPKLHAGELPPGIVSLNRAIGRALRRQRGADFQYYDKPAGDLKLREQ 168

Query: 95  LAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYE 154
           L   + KR   P++  ++ ITSG Q AL L        GD+V VE+P +   LQ  +   
Sbjct: 169 LGLLLAKR-GWPVTPDELCITSGCQHALFLALMACCQRGDVVAVESPGFYGVLQLLEQLG 227

Query: 155 PEFVQIPLDD-EGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLE 213
            + ++IP     GM +D LEE L         ++     P F  P G  MSE  R+RL+ 
Sbjct: 228 LQVMEIPTSTASGMDMDALEEALGRWN-----IQACVVSPAFATPGGALMSEAPRRRLMA 282

Query: 214 LASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEP 273
           LA +YD  ++ED+ Y E  +S  P   +KA D+  RV++  +FSK+L+   R+GWI+   
Sbjct: 283 LAEKYDLAVIEDDIYAESGFSRVP-DTLKALDENNRVIHCSSFSKVLSRDLRLGWISGAR 341

Query: 274 HLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFM 333
              R L + K    L ++ + Q     Y+E G L  H+    +    +RD +L +L  + 
Sbjct: 342 WHQRILHL-KMVTQLASSRYLQQGVAAYMEEGELSAHLRRQRKVLSEQRDRLLASLLAW- 399

Query: 334 PEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFT 393
           P  VR T P+GG+ VW+ LP  +DT  +  KA+  GV   PG  F A     N +R++F+
Sbjct: 400 PVSVRVTAPQGGLAVWLELPATVDTLAVYPKALDAGVVITPGPLFSASGKYGNCLRISFS 459

Query: 394 YVPEEKIREGIKRLAETI 411
           +  +E+    + +L E +
Sbjct: 460 HPWDERRIRALNQLPELL 477


Lambda     K      H
   0.318    0.137    0.398 

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: 454
Number of extensions: 24
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: 417
Length of database: 480
Length adjustment: 33
Effective length of query: 384
Effective length of database: 447
Effective search space:   171648
Effective search space used:   171648
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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