GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvD in Burkholderia phytofirmans PsJN

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate BPHYT_RS25650 BPHYT_RS25650 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25650 BPHYT_RS25650
           dihydroxy-acid dehydratase
          Length = 588

 Score =  430 bits (1106), Expect = e-125
 Identities = 236/563 (41%), Positives = 332/563 (58%), Gaps = 15/563 (2%)

Query: 6   RSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAI 65
           RS+ +T GV R+P+R+   A G   E   KP V I +     TPC+  L +++D     I
Sbjct: 8   RSRRVTDGVTRAPHRAFLRATGLDDESMQKPFVAIVDTFGENTPCSMSLNQVSDNVRLGI 67

Query: 66  KASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDK 125
            A    P      ++SDG SM   GM+ SL+SREV+AD +E   +    D ++ + GCDK
Sbjct: 68  AAGGGVPIRGSAISVSDGTSMNHSGMRMSLVSREVVADSVELFVRAHNYDALIGVAGCDK 127

Query: 126 NMPGGMIALARTNVPGIYVYGGTIKPGNWKG-----------KDLTIVSSFEAVGEFTAG 174
            +PG ++ + R NVPG++++GG + PG   G           +  TI+++ EAVG    G
Sbjct: 128 TLPGILMGMVRVNVPGVFLFGGAMLPGVAPGQLPGGAGTGLQRQSTILTTIEAVGTTQRG 187

Query: 175 RMSQEDFEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAE 234
            MS+   + +EK   P+ GSC G +TANTM+   E LG++ L S+ +     E++  A  
Sbjct: 188 DMSRAQLDAIEKQCTPTAGSCPGQFTANTMAMVAETLGLAPLGSAMVPAVYSERIAIARR 247

Query: 235 SARVLVEAIKQDIK-PRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDD 293
           +   ++  + Q    PRD++T +S+ENA A + ATGGSTNA LH  AIA+ A + + +DD
Sbjct: 248 AGETVMRILTQGGPLPRDLVTMESLENACAAVAATGGSTNAALHIPAIANEAGIRFALDD 307

Query: 294 FERIRRKVPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEEL 353
            +R+  K+P+I +L+P G+Y+A DLH AGG+P V+  LL  G LHGD     G TLAE L
Sbjct: 308 VQRVFAKIPLIGDLQPGGRYLAQDLHHAGGVPAVLNALLAGGFLHGDVPAFGGGTLAEAL 367

Query: 354 ENVPDTPRADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFED 413
                    D  V+ P ++ L   G L IL+GNLA +GA  KI GLK+   TG  RVFE 
Sbjct: 368 SAFSGP---DGIVVRPCDEPLGENGGLVILRGNLAPDGACLKIAGLKSLSFTGAVRVFEC 424

Query: 414 EQSAMEAILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFS 473
           E+  M  + A     GD+LV+R  GPKGGPGM EML  T+AI G+G+GE V  +TDGRFS
Sbjct: 425 EEDCMAVVAARDYREGDVLVIRNEGPKGGPGMREMLGVTAAIYGQGMGEKVALLTDGRFS 484

Query: 474 GGTWGMVVGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAP 533
           G T GM +G+V PEA  GG I L++  D + IDA   +L+++++D+ELARRRA+    A 
Sbjct: 485 GATRGMCIGYVGPEAAAGGPIGLLRNDDRVHIDARAGILRVDLSDDELARRRADAPARAS 544

Query: 534 RYTRGVLAKFSKLASTASKGAVT 556
           R   GVL K+  L   A  GAVT
Sbjct: 545 RRLAGVLEKYEALVRPAHLGAVT 567


Lambda     K      H
   0.316    0.133    0.386 

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: 956
Number of extensions: 48
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 557
Length of database: 588
Length adjustment: 36
Effective length of query: 521
Effective length of database: 552
Effective search space:   287592
Effective search space used:   287592
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 (21.6 bits)
S2: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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