Alignments for a candidate for ilvD in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Herbaspirillum seropedicae SmR1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__HerbieS:HSERO_RS16705
          Length = 578

 Score =  371 bits (953), Expect = e-107
 Identities = 219/530 (41%), Positives = 328/530 (61%), Gaps = 16/530 (3%)

Query: 31  RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGIAMGHEGMRYS 90
           RP+IG+ N+++E+ P + H   +AE VK GI  AGG PLEF  +++ + + +    M Y 
Sbjct: 43  RPVIGICNTYSELTPCNSHFRALAEQVKIGIWEAGGFPLEFPVMSLGETL-LRPTAMLY- 100

Query: 91  LPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILINGGPMMPGVY 150
              R + +  VE  + A+ LD VV++  CDK TP  L+ AA ++VP I ++GGPM+ G Y
Sbjct: 101 ---RNLASMDVEESIRANPLDGVVLLMGCDKTTPALLMGAASVDVPTIGVSGGPMLSGKY 157

Query: 151 GKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANTMNMLSEAMGL 208
               +     + +M+  ++ G+   EE  + E       G C  + TA+TM  + EA+G+
Sbjct: 158 RGRELGSGTGVWQMSEDVRAGKMTQEEFFEAESCMHRSHGHCMTMGTASTMASMVEALGV 217

Query: 209 MLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIAVDMALGGSTN 268
            LP  + +PAV+ARR   A+  G RIV+MVEE L   KILTR+A ENAI V+ A+GGSTN
Sbjct: 218 GLPHNAAIPAVDARRNVLARNAGRRIVQMVEEDLVLSKILTRQAFENAIRVNAAIGGSTN 277

Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328
           +V+HL A+A  +GI L L+ +D+I +++P +  + PSG+  + D   AGG+PAV+++L  
Sbjct: 278 AVIHLLAIAGRIGIKLDLKDWDDIGQQLPCLLDLQPSGKFLMEDFYYAGGLPAVIRQL-- 335

Query: 329 AGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGSLAPNGAVVKA 388
             +I K ALT  GKT+WEN +DA   + EVIR  D P+    G+AILKG+LAP+GAV+K 
Sbjct: 336 ESVIDKTALTANGKTLWENCQDAPNWNEEVIRSFDKPFKEAAGIAILKGNLAPDGAVIKP 395

Query: 389 SAVKRELWKFKGVARVFDREEDAVKAI--RGGEIEPGTVIVIRYEGPRGGPGMREM--LT 444
           SA    L K +G A VF+  +D  K I     +++   V+V++  GP+G PGM E   + 
Sbjct: 396 SAATPALLKHRGRAVVFENSDDLHKRIDDENLDVDETCVLVLKNCGPKGYPGMAEAGNMP 455

Query: 445 ATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGGPIALVQDGDEIVIDIEKR 504
               ++  G+ D V  V+D R SG   G  + HVSPEAAAGGP+A+VQ+GD I +D+E R
Sbjct: 456 LPPKILRKGITDMVR-VSDARMSGTAYGTVVLHVSPEAAAGGPLAVVQNGDFIELDVEAR 514

Query: 505 RLDLLVDEKELEERRARW-KPKVKP-LRRGILRRYAKMALSADKGGALEY 552
           +L L V ++EL  RRA+W KP++ P ++RG ++ Y      A++G  L++
Sbjct: 515 KLHLDVSDEELARRRAQWQKPELPPQMQRGWVKLYVDHVQQANQGADLDF 564


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: 812
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: 578
Length adjustment: 36
Effective length of query: 516
Effective length of database: 542
Effective search space:   279672
Effective search space used:   279672
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