GapMind for Amino acid biosynthesis

 

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

Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate H281DRAFT_01831 H281DRAFT_01831 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain

Query= reanno::Koxy:BWI76_RS24235
         (393 letters)



>FitnessBrowser__Burk376:H281DRAFT_01831
          Length = 414

 Score =  292 bits (748), Expect = 1e-83
 Identities = 158/381 (41%), Positives = 230/381 (60%), Gaps = 6/381 (1%)

Query: 16  SAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAFQYGLTEGYPPL 75
           S +REL K+   PG+IS  GG PA +LFD +GL  A  +      N   QYG T+G P L
Sbjct: 25  SPIRELFKYLGEPGMISFAGGYPASDLFDVDGLQQAEARAYQDP-NSCLQYGPTDGLPRL 83

Query: 76  RQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAALQVFQL 135
           +  +  L   RGV C  + + +T+GSQQ LD++ R L+ PGD +  E+P Y A LQ  +L
Sbjct: 84  KHELISLMARRGVPCALNEMLVTTGSQQGLDLLLRVLVSPGDVVFTEQPAYPATLQALKL 143

Query: 136 AQANILSVDTDDDGMLVEQLADLLETTRV---KAVYLVPTFGNPGGKTLSEARRRRLVEL 192
            QA I++V  D  G+ V+ LA+LL + RV   K +Y VPTF NP G T++  RR  L++L
Sbjct: 144 QQAKIVTVPVDAHGLDVDHLAELLASGRVARPKLLYTVPTFANPTGATITRERRIALLKL 203

Query: 193 AKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVEL-GCEDQVVYTSTFSKILAPGMRIGWI 251
           A ++ F+I+EDDPYG++ F+      +   A E+ G  D VV+ ++ SKI+APG+R+GW 
Sbjct: 204 AVQYKFLIVEDDPYGDLRFSGVAVPSIISLAAEVEGSRDWVVHFASLSKIVAPGLRVGWT 263

Query: 252 VMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALADAL 311
           + P  + ++ VI KQ  DL +   +Q I AEYL+   LE  +  I E Y +KC AL +AL
Sbjct: 264 IAPAEITRRCVIAKQTVDLCSAPWTQAIAAEYLADGALERHLPRITEMYGRKCEALCEAL 323

Query: 312 ESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDNPDTRTLR 371
            SQ G+ L+F RP GGMF+WAR     D    ++  +EN V++VPG+AF+ D  D  +LR
Sbjct: 324 RSQFGDTLQFHRPDGGMFVWARIE-GIDASALLQHAIENKVMFVPGKAFFADRIDPASLR 382

Query: 372 LSYSTVSADGLMTAVERLAKS 392
           LS++      +    +RL ++
Sbjct: 383 LSFAAPGIADIEEGAKRLRRA 403


Lambda     K      H
   0.320    0.136    0.395 

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: 425
Number of extensions: 20
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: 393
Length of database: 414
Length adjustment: 31
Effective length of query: 362
Effective length of database: 383
Effective search space:   138646
Effective search space used:   138646
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 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