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_RS22480 HSERO_RS22480 dihydroxy-acid dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__HerbieS:HSERO_RS22480
          Length = 594

 Score =  281 bits (718), Expect = 7e-80
 Identities = 193/573 (33%), Positives = 301/573 (52%), Gaps = 30/573 (5%)

Query: 2   KRSDVFLRPEYAPHRALWRAS----GLIDEELR--RPLIGVANSWNEIVP-GHVHLDKVA 54
           +  D F  P++    AL+       G+  EELR  RP+IG+A S ++I P   +HL+ +A
Sbjct: 12  RSQDWFDNPDHIDMTALYLERFMNYGITAEELRSGRPIIGIAQSGSDISPCNRIHLE-LA 70

Query: 55  EAVKAGIRMAGGTPLEFGTIAVCDGIAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVV 114
           + V+ GIR AGG P+EF    + +        +  +L         VEI+   + +DAVV
Sbjct: 71  KRVRDGIRDAGGIPMEFPLHPIFENCRRPTAAIDRNL----AYLGLVEIL-HGYPIDAVV 125

Query: 115 MVTNCDKITPGFLLAAARLEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE 174
           + T CDK TP  ++AAA +++P I+++GGPM+ G    E +     + +   L+  G  +
Sbjct: 126 LTTGCDKTTPSQIMAAATVDIPAIVLSGGPMLDGWMDGELVGSGSAIWKGRKLLSAGSID 185

Query: 175 ELRKLEESALPGP--GSCAGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGM 232
             + LE +A   P  G C  + TA+TMN ++EA+G+ L G S +PA    R   A  TG 
Sbjct: 186 NEKFLEIAAASAPSSGHCNTMGTASTMNAMAEALGMSLTGCSAIPAPYRERGQMAYETGR 245

Query: 233 RIVKMVEEGLTPDKILTRKALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEI 292
           RIV M  E L P  ILTR A  +AI V+ A+GGSTN+  H+ A+A   G++L  E + + 
Sbjct: 246 RIVGMAYEDLRPSAILTRDAFLDAIVVNAAIGGSTNAQPHIMAMARHAGVELQSEDWMKY 305

Query: 293 SRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAA 352
              VP + ++ P+G++      RAGG+PA++ EL +AG +  + +T TGKT+ EN++  A
Sbjct: 306 GYDVPLLLNMQPAGKYLGERFHRAGGVPAIMWELQQAGKLRAERITATGKTMAENLQGRA 365

Query: 353 VLDREVIRPLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWK-----------FKGV 401
             DRE+I P   P     G  +LKG+L  + A++K S +     +           F+  
Sbjct: 366 SNDREMIYPFAAPLRERAGFLVLKGNLF-DFAIMKTSVISETFRERYLSTPGQENIFECR 424

Query: 402 ARVFDREEDAVKAIRGG--EIEPGTVIVIRYEGPRGGPGMREMLTATAAVMALGLG-DKV 458
           A VFD  +D    I     +I+  T++ IR  GP G PG  E++        +  G   +
Sbjct: 425 AVVFDGSDDYHARINDPALKIDENTLLAIRGAGPVGWPGSAEVVNMQPPDALIKRGVSTL 484

Query: 459 ALVTDGRFSGATRGPAIGHVSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518
             + DGR SG +  P+I + SPE+A GG +A ++DGD + ID+     ++LV E+EL  R
Sbjct: 485 PTLGDGRQSGTSDSPSILNASPESAVGGGLAYLRDGDRVRIDLNTGECNMLVSEEELARR 544

Query: 519 RARWKPKVKPLRRGILRRYAKMALSADKGGALE 551
           ++   P V P +      Y       + G  +E
Sbjct: 545 KSEGIPPVPPSQTPWQEIYRSTVGQLETGACME 577


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: 787
Number of extensions: 35
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: 552
Length of database: 594
Length adjustment: 36
Effective length of query: 516
Effective length of database: 558
Effective search space:   287928
Effective search space used:   287928
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 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