Alignments for a candidate for ilvD in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Cupriavidus basilensis 4G11

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate RR42_RS33950 RR42_RS33950 dihydroxy-acid dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__Cup4G11:RR42_RS33950
          Length = 577

 Score =  373 bits (957), Expect = e-107
 Identities = 220/547 (40%), Positives = 324/547 (59%), Gaps = 16/547 (2%)

Query: 15  HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73
           +R+  +  G+ D E   RP+IG+ N+W+E+ P + H  K+AE VK G+  AGG P+EF  
Sbjct: 24  YRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGVYEAGGFPVEFPV 83

Query: 74  IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132
            +       G   +R  ++ +R + A  VE  +  + +DAVV++T CDK TP  L+ AA 
Sbjct: 84  FS------NGESNLRPTAMLTRNLAAMDVEEAIRGNPIDAVVLLTGCDKTTPALLMGAAS 137

Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGR--TEELRKLEESALPGPGSC 190
            +VP I++ GGPM+ G    + I     + +++  +K G     +    E       G+C
Sbjct: 138 CDVPAIVVTGGPMLNGKLDGKNIGSGTAVWQLHESLKAGEINVHQFLSAEAGMSRSAGTC 197

Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250
             + TA+TM  ++EA+G  LP  + +PAV++RR   A ++G+RIV+M +EGLT  KILTR
Sbjct: 198 NTMGTASTMACMAEALGTSLPHNAAIPAVDSRRYVLAHMSGIRIVEMAKEGLTLSKILTR 257

Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310
            A ENAI  + A+GGSTN+V+HL+A+A  +G+ L LE +  I R  P I  + PSGR  +
Sbjct: 258 AAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWTRIGRDTPTIVDLMPSGRFLM 317

Query: 311 VDLDRAGGIPAVLKELGEAGLI-HKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPF 369
            +   AGG+PAVL+ LGEA L+ H DALTV G+T+W+NVKDA   + EVIR LDNP    
Sbjct: 318 EEFYYAGGLPAVLRRLGEANLLPHPDALTVNGRTLWQNVKDAPNTNDEVIRALDNPLMAD 377

Query: 370 GGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAI--RGGEIEPGTVIV 427
           GG+ +L+G+LAP GAV+K SA    L K +G A VF+  E   + I     +++  +V+V
Sbjct: 378 GGIRVLRGNLAPRGAVLKPSAATPGLLKHRGRAVVFENLEHYKERIVDETLDVDASSVMV 437

Query: 428 IRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAG 485
           ++  GP+G PGM E+  +     ++  G+ D V  ++D R SG   G  + HV+PEAAAG
Sbjct: 438 LKNCGPKGYPGMAEVGNMGLPPKLLRQGVKDMVR-ISDARMSGTAYGTVVLHVAPEAAAG 496

Query: 486 GPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSAD 545
           GP+A V+DGD I +D E   L L +D++EL  R A           G  R Y    L AD
Sbjct: 497 GPLAAVRDGDWIELDCEAGTLHLDIDDEELARRMAERVDTRAAGEGGYRRLYVDHVLQAD 556

Query: 546 KGGALEY 552
           +G  L++
Sbjct: 557 EGCDLDF 563


Lambda     K      H
   0.319    0.138    0.401 

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: 863
Number of extensions: 36
Number of successful extensions: 6
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: 552
Length of database: 577
Length adjustment: 36
Effective length of query: 516
Effective length of database: 541
Effective search space:   279156
Effective search space used:   279156
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis