GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Clostridium tyrobutyricum FAM22553

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_017752781.1 PN53_RS06145 PLP-dependent aminotransferase family protein

Query= BRENDA::A0A060PQX5
         (417 letters)



>NCBI__GCF_000816635.1:WP_017752781.1
          Length = 481

 Score =  197 bits (500), Expect = 7e-55
 Identities = 118/369 (31%), Positives = 198/369 (53%), Gaps = 10/369 (2%)

Query: 46  VISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDI 105
           +IS     P  + F VE   +     + +   + L YG  +G+  L   L ++M  +  I
Sbjct: 118 MISFKSIAPDDKLFDVENFKKSFLNCISREGGKILNYGYAQGYKSLIKYLLKYMENK-GI 176

Query: 106 PISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDE 165
             ++ DI+IT+G  +  DLI     N GD V+ E PT+  A++  K ++   V + +D++
Sbjct: 177 NTTEKDIIITNGFTEGFDLILSCLTNAGDSVICENPTHNTAIKIMKLHKLNIVGVAMDED 236

Query: 166 GMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVED 225
           G+ +  L+ KL       +K KL Y IP++ NP G+ M  ++R +L  +  E +  IVED
Sbjct: 237 GINLKDLKIKLTR-----QKPKLSYFIPSYHNPTGIVMPPEKRTKLYNILRENNIPIVED 291

Query: 226 NPYGELRYSGEPVKPIKAWDDEGR-VMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQ 284
               ELRY  + V PI A    G  V+Y+G+FSKIL PG RIGWI A+  LI  +E  K+
Sbjct: 292 GFNEELRYLSDHVSPIAALSGNGNSVIYIGSFSKILFPGIRIGWILADKQLIGYIESLKR 351

Query: 285 SVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEG 344
           S ++ T+   Q + + Y++ G+ + +I  +  FYK + +  +    +++P    +   EG
Sbjct: 352 SRNIHTSFLDQAVFYDYLKEGNFEKYIKKVRRFYKDKYEKAIDFARKYIPYSKIY--GEG 409

Query: 345 GMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGI 404
           G+ +++ +  GID++ +L +   +GV + PG+ F+      NT RL F+ V +E I  G 
Sbjct: 410 GLHIFIEV-YGIDSRKLLNRCCKRGVIFTPGDIFYTDGGGGNTFRLGFSRVSDEDIERGF 468

Query: 405 KRLAETIKE 413
           K + E IK+
Sbjct: 469 KIIGEEIKK 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: 477
Number of extensions: 21
Number of successful extensions: 4
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: 481
Length adjustment: 33
Effective length of query: 384
Effective length of database: 448
Effective search space:   172032
Effective search space used:   172032
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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