GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Marino:GFF1728
          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 Aug 03 2021. The underlying query database was built on Aug 03 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