Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2C3

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate AO356_13250 AO356_13250 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13250
          Length = 613

 Score =  939 bits (2428), Expect = 0.0
 Identities = 464/608 (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  GGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIERVGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 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++++ +A
Sbjct: 299 IDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKSMAEA 358

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

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

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

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           VR+GD + IDIPNR+I+L +S+ ELA RR EQD KGW P EVR R VTTALKAYA  ATS
Sbjct: 539 VRDGDKVLIDIPNRSINLLISDEELAGRRIEQDNKGWKPVEVRPRKVTTALKAYALLATS 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: 1198
Number of extensions: 32
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 AO356_13250 AO356_13250 (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.346456.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                   -----------
   1.8e-254  831.2   1.3   2.1e-254  831.0   1.3    1.0  1  FitnessBrowser__pseudo5_N2C3_1:AO356_13250  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo5_N2C3_1:AO356_13250  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  831.0   1.3  2.1e-254  2.1e-254       2     542 ..      18     606 ..      17     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 831.0 bits;  conditional E-value: 2.1e-254
                                   TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGia 68 
                                                 aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eie+ Ggvakefntiav+DGia
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250  18 ARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERVGGVAKEFNTIAVDDGIA 84 
                                                 79***************************************************************** PP

                                   TIGR00110  69 mgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeag 135
                                                 mgh+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniP+i+vsGGpmeag
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250  85 MGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFVSGGPMEAG 151
                                                 ******************************************************************* PP

                                   TIGR00110 136 ktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgs 202
                                                 ktkl    + +d+++a++ +a++  s+e++ e+ersacPt+gsCsG+ftansm+cltealGl+lPg+
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 152 KTKL--ASHGLDLVDAMVIAADSSASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGLALPGN 216
                                                 ***8..557899******************************************************* PP

                                   TIGR00110 203 stllatsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhl 262
                                                 +++lat++++++l+ ++g++ivel+k+++        Pr+i++ +afena+tld+a+GGstnt+Lhl
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 217 GSTLATHSDREQLFLQAGRTIVELCKRYYGendesvlPRNIANFKAFENAMTLDIAMGGSTNTILHL 283
                                                 *****************************99999********************************* PP

                                   TIGR00110 263 laiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltv 328
                                                 la+a+ea+++++l d+drlsr+vP+l+k++P+ +k+ +ed+hraGG+ ++l++l + gllh+d  tv
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 284 LAAAQEAEIDFDLRDIDRLSRHVPQLCKVAPNIQKYhMEDVHRAGGIFSILGSLARGGLLHTDLPTV 350
                                                 *********************************9999****************************** PP

                                   TIGR00110 329 tGktlaetlekvkvlr...................................vdqdvirsldnpvkke 360
                                                   k++ae ++k ++++                                    ++ +irs+++++++e
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 351 HSKSMAEAIAKWDITQttdeavhhffkagpagiptqtafsqstrwdtldddRENGCIRSVEHAYSQE 417
                                                 **************999******************************77555555************ PP

                                   TIGR00110 361 gglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGg 427
                                                 gglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +il+ +vk+Gd+v+iryeGPkGg
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 418 GGLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRYEGPKGG 484
                                                 ******************************************************************* PP

                                   TIGR00110 428 PGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDien 494
                                                 PGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv+dGDk+ iDi+n
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 485 PGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGDKVLIDIPN 551
                                                 ******************************************************************* PP

                                   TIGR00110 495 rkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                                 r ++l +s+eela rr ++++k++       r+v  aL++ya l++sadkGav++
  FitnessBrowser__pseudo5_N2C3_1:AO356_13250 552 RSINLLISDEELAGRRIEQDNKGWkpvevrpRKVTTALKAYALLATSADKGAVRN 606
                                                 ***********************999***9999********************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 26.71
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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