Alignments for a candidate for ilvD in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Azospirillum brasilense Sp245

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>FitnessBrowser__azobra:AZOBR_RS15015
          Length = 621

 Score =  962 bits (2487), Expect = 0.0
 Identities = 477/615 (77%), Positives = 531/615 (86%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRT+THGRNMAGARGLWRATGMKD DFGKPIIA+ANSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPHYRSRTSTHGRNMAGARGLWRATGMKDGDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSR+LIAD+VEYMVNAHCADA+VCIS
Sbjct: 61  AREIEKAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADAVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAAMRLNIP VFVSGGPMEAGKV  +GK +A+DL+DAMV AAD + SDEE
Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVNWRGKTKAVDLIDAMVAAADPTVSDEE 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
              +E+ +CPTCGSCSGMFTANSMNCLTEALGLSLPGNG++LATHADR+ LF  AGR+ V
Sbjct: 181 AAVMERGSCPTCGSCSGMFTANSMNCLTEALGLSLPGNGTILATHADRKELFLAAGRMAV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
           +LC+RWY++EDATALPRGIAT  AFENAM+LDIAMGGSTNTVLHLLAAA EG + F+MAD
Sbjct: 241 ELCRRWYQEEDATALPRGIATFEAFENAMTLDIAMGGSTNTVLHLLAAAQEGQVPFTMAD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSR VP + KVAPA SDVH+EDVH+AGG+  ILGEL+RGGL++    TVHA T+G+A
Sbjct: 301 IDRLSRRVPNVCKVAPAVSDVHIEDVHKAGGIFGILGELDRGGLLNRDVATVHAKTLGDA 360

Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420
           L RWD+ RT  +  H  FKAAPGG PT +AFSQ  RW ELDLDR+ GVIRSV+  FSKDG
Sbjct: 361 LDRWDVKRTQDEGVHTMFKAAPGGIPTTIAFSQEKRWPELDLDRDKGVIRSVDSAFSKDG 420

Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480
           GLAVLFGN+A +GCIVKTAGVD S L F G ARVFESQDAAV  ILG  VKAG+VVVIRY
Sbjct: 421 GLAVLFGNIAEKGCIVKTAGVDASNLVFAGPARVFESQDAAVEAILGDTVKAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540
           EGP+GGPGMQEMLYPT+YLKSKGLG ACALVTDGRFSGGTSGLSIGH SPEA +GG I L
Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIGL 540

Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600
           V+ GD I IDIP R I L +SD  L  RR+A+ A+G DAW P NR R ++PALRAYAA+T
Sbjct: 541 VQDGDRIEIDIPNRKINLALSDEELQRRRDAENAKGADAWKPANRNRVVSPALRAYAALT 600

Query: 601 TNAARGAVRDVSQIE 615
           T+A RGAVRDVSQ+E
Sbjct: 601 TSADRGAVRDVSQVE 615


Lambda     K      H
   0.318    0.134    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: 1372
Number of extensions: 49
Number of successful extensions: 1
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: 617
Length of database: 621
Length adjustment: 37
Effective length of query: 580
Effective length of database: 584
Effective search space:   338720
Effective search space used:   338720
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate AZOBR_RS15015 AZOBR_RS15015 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.3095.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.7e-253  826.0   2.1   7.8e-253  825.8   2.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS15015  AZOBR_RS15015 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS15015  AZOBR_RS15015 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.8   2.1  7.8e-253  7.8e-253       2     542 ..      18     610 ..      17     611 .. 0.99

  Alignments for each domain:
  == domain 1  score: 825.8 bits;  conditional E-value: 7.8e-253
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar l++atG+kd d++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg
  lcl|FitnessBrowser__azobra:AZOBR_RS15015  18 ARGLWRATGMKDGDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMG 86 
                                               689****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaD+ve++v+ah++Dalv+is+CDki+PGmlmaa+rlniPa++vsGGpmeagk++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS15015  87 HDGMLYSLPSRELIADAVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVNW 155
                                               ********************************************************************* PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                                 k + vd+++a++++a++ +s+ee   +er +cPt+gsCsG+ftansm+cltealGlslPg++t+lat
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 156 RGKTKAVDLIDAMVAAADPTVSDEEAAVMERGSCPTCGSCSGMFTANSMNCLTEALGLSLPGNGTILAT 224
                                               ********************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a++kel+  +g+  vel+++ ++       Pr i+t eafena+tld+a+GGstntvLhlla+a+e +
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 225 HADRKELFLAAGRMAVELCRRWYQeedatalPRGIATFEAFENAMTLDIAMGGSTNTVLHLLAAAQEGQ 293
                                               ***********************99******************************************** PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               v +++ d+drlsr+vP ++k++P+ + v ied+h+aGG+ ++l+eld+ gll++d+ tv  ktl++ l+
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 294 VPFTMADIDRLSRRVPNVCKVAPAVSDVhIEDVHKAGGIFGILGELDRGGLLNRDVATVHAKTLGDALD 362
                                               ************************88887**************************************** PP

                                 TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372
                                               + +v+r                                    d+ virs+d++++k+gglavL+Gn+ae
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 363 RWDVKRtqdegvhtmfkaapggipttiafsqekrwpeldldRDKGVIRSVDSAFSKDGGLAVLFGNIAE 431
                                               *****9*******************************99666666************************ PP

                                 TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441
                                               +G++vk+agv+ + l+f Gpa+vfes+++a+eailg  vk+GdvvviryeGP+GgPGm+emL+Pts+l+
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 432 KGCIVKTAGVDASNLVFAGPARVFESQDAAVEAILGDTVKAGDVVVIRYEGPRGGPGMQEMLYPTSYLK 500
                                               ********************************************************************* PP

                                 TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                               + GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv+dGD+i+iDi+nrk++l++s+eel++rr
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 501 SKGLGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIGLVQDGDRIEIDIPNRKINLALSDEELQRRR 569
                                               ********************************************************************* PP

                                 TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542
                                               ++ ++k+a         r v+ aL++ya l +sad+Gav+d
  lcl|FitnessBrowser__azobra:AZOBR_RS15015 570 DAENAKGAdawkpanrnRVVSPALRAYAALTTSADRGAVRD 610
                                               *****999999****999*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (621 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 13.00
//
[ok]

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