Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2E3

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate AO353_08345 AO353_08345 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08345
          Length = 613

 Score =  940 bits (2430), Expect = 0.0
 Identities = 465/608 (76%), Positives = 521/608 (85%), Gaps = 2/608 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS+T+THGRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA+LRLNIP +FVSGGPMEAGK  +   +H LDLVDAMV AAD   SDE 
Sbjct: 121 NCDKITPGMLMAALRLNIPVIFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEK 178

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           V   ERSACPTCGSCSGMFTANSMNCLTEALGL+LPGNGSTLATH DR++LF++AG  IV
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHSDREQLFLQAGRTIV 238

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           +L +RYY ++D   LPR IA+ +AFENAMTLDIAMGGSTNT+LH+LAAA E EIDF + D
Sbjct: 239 ELCKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRD 298

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           ID LSR VP L KVAP     HMEDVHRAGGI SILG L +GGLL+ D PTVH++T+ + 
Sbjct: 299 IDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKTMAEG 358

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           I +WDIT+T  E V  F++A P GIPTQ AFSQ  RW+ LD DRENG IRSVEH +S++G
Sbjct: 359 IAKWDITQTTDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSQEG 418

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GN+A+DGC+VKTAGVDESI  F G A++FESQD++V+ ILA+EVK GD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKEGDIVIIRY 478

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGPKGGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGHASPEAA GG IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           VR+GD + IDIPNR+I+L VS+ ELAARR EQD KGW P EVR R VTTALKAYA  ATS
Sbjct: 539 VRDGDKVLIDIPNRSINLLVSDEELAARRVEQDKKGWKPVEVRPRKVTTALKAYALLATS 598

Query: 601 ADRGAVRD 608
           AD+GAVR+
Sbjct: 599 ADKGAVRN 606


Lambda     K      H
   0.318    0.134    0.391 

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: 1208
Number of extensions: 33
Number of successful extensions: 2
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: 612
Length of database: 613
Length adjustment: 37
Effective length of query: 575
Effective length of database: 576
Effective search space:   331200
Effective search space used:   331200
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 AO353_08345 AO353_08345 (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.11380.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.9e-256  837.8   1.3   2.2e-256  837.6   1.3    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345  AO353_08345 dihydroxy-acid dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345  AO353_08345 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  837.6   1.3  2.2e-256  2.2e-256       2     542 ..      18     606 ..      17     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 837.6 bits;  conditional E-value: 2.2e-256
                                     TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDG 66 
                                                   aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345  18 ARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDG 82 
                                                   79*************************************************************** PP

                                     TIGR00110  67 iamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGp 131
                                                   iamgh+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniP+i+vsGGp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345  83 IAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFVSGGP 147
                                                   ***************************************************************** PP

                                     TIGR00110 132 meagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealG 196
                                                   meagktkl    + +d+++a++ +a++  s+e++ e+ersacPt+gsCsG+ftansm+cltealG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 148 MEAGKTKL--ASHGLDLVDAMVIAADSSASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALG 210
                                                   *******8..557899************************************************* PP

                                     TIGR00110 197 lslPgsstllatsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGG 254
                                                   l+lPg++++lat++++++l+ ++g++ivel+k+++        Pr+i++ +afena+tld+a+GG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 211 LALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGendesvlPRNIANFKAFENAMTLDIAMGG 275
                                                   ***********************************99999************************* PP

                                     TIGR00110 255 stntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldke 318
                                                   stnt+Lhlla+a+ea+++++l d+drlsr+vP+l+k++P+ +k+ +ed+hraGG+ ++l++l + 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 276 STNTILHLLAAAQEAEIDFDLRDIDRLSRHVPQLCKVAPNIQKYhMEDVHRAGGIFSILGSLARG 340
                                                   *****************************************9999******************** PP

                                     TIGR00110 319 gllhkdaltvtGktlaetlekvkvlr...................................vdqd 348
                                                   gllh+d  tv  kt+ae ++k ++++                                    ++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 341 GLLHTDLPTVHSKTMAEGIAKWDITQttdeavhhffkagpagiptqtafsqstrwetldddRENG 405
                                                   ************************999******************************77555555 PP

                                     TIGR00110 349 virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                   +irs+++++++egglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +il+ +vke
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 406 CIRSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKE 470
                                                   ***************************************************************** PP

                                     TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGa 478
                                                   Gd+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 471 GDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGA 535
                                                   ***************************************************************** PP

                                     TIGR00110 479 ialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssad 536
                                                   i+lv+dGDk+ iDi+nr ++l vs+eela+rr +++kk++       r+v  aL++ya l++sad
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 536 IGLVRDGDKVLIDIPNRSINLLVSDEELAARRVEQDKKGWkpvevrpRKVTTALKAYALLATSAD 600
                                                   ****************************************9****9999**************** PP

                                     TIGR00110 537 kGavld 542
                                                   kGav++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08345 601 KGAVRN 606
                                                   ****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (613 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: 12.72
//
[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