Aligments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2E2

Align dihydroxyacid dehydratase (characterized)
to candidate Pf6N2E2_4564 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564
          Length = 613

 Score =  916 bits (2368), Expect = 0.0
 Identities = 460/617 (74%), Positives = 519/617 (84%), Gaps = 6/617 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS T+THGRNMAGARALWRATGM D DF KPIIA+ NSFTQFVPGHVHL+DLG+LV
Sbjct: 1   MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IE  GGVAKEFNTIAVDDGIAMGH GMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIERVGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA+LRLNIPVIFVSGGPMEAGKTKL+     LDLVDAM+  AD   SD +
Sbjct: 121 NCDKITPGMLMAALRLNIPVIFVSGGPMEAGKTKLASH--GLDLVDAMVIAADSSASDEK 178

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
             + ERSACPTCGSCSGMFTANSMNCLTEALGL+ PGNGS LATH+DR+QLFL AG+ IV
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHSDREQLFLQAGRTIV 238

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           EL KRYY +NDES LPRNIA+  AFENAMTLDIAMGGSTNT+LHLLAAAQEAEIDF + D
Sbjct: 239 ELCKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRD 298

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           ID+LSR VPQLCKVAP+ QKYHMEDVHRAGG+  ILG L R GLL+ D+  V   T+ + 
Sbjct: 299 IDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKTMAEA 358

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           + ++D+  T D+AV + F+AGPAGI T  AFSQ  RW+TLDDDR NGCIRS+EHAYSK+G
Sbjct: 359 IAKWDITQTTDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSKEG 418

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVLYGN A +GC+VKTAGVD+SI  F G AK++ESQD AV  IL  +V AGD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRY 478

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPTS+LKS GLGKACAL+TDGRFSGGTSGLSIGH SPEAA+GG+IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTP-KNRERQVSFALRAYASL 599
           + DGD + IDIPNR I L +SD ELA RR  QD   +K W P + R R+V+ AL+AYA L
Sbjct: 539 VRDGDKVLIDIPNRSINLLISDEELAGRRVEQD---NKGWKPVEVRPRKVTTALKAYALL 595

Query: 600 ATSADKGAVRDKSKLGG 616
           ATSADKGAVR+K+ L G
Sbjct: 596 ATSADKGAVRNKAMLDG 612


Lambda     K      H
   0.317    0.134    0.386 

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: 1201
Number of extensions: 44
Number of successful extensions: 4
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: 616
Length of database: 613
Length adjustment: 37
Effective length of query: 579
Effective length of database: 576
Effective search space:   333504
Effective search space used:   333504
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 Pf6N2E2_4564 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
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.3958.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.4e-255  832.9   1.4   6.3e-255  832.7   1.4    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564  Dihydroxy-acid dehydratase (EC 4


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564  Dihydroxy-acid dehydratase (EC 4.2.1.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  832.7   1.4  6.3e-255  6.3e-255       2     542 ..      18     606 ..      17     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 832.7 bits;  conditional E-value: 6.3e-255
                                      TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsD 65 
                                                    aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eie+ Ggvakefntiav+D
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564  18 ARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERVGGVAKEFNTIAVDD 81 
                                                    79************************************************************** PP

                                      TIGR00110  66 GiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsG 129
                                                    Giamgh+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniP+i+vsG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564  82 GIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFVSG 145
                                                    **************************************************************** PP

                                      TIGR00110 130 GpmeagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmaclte 193
                                                    Gpmeagktkl    + +d+++a++ +a++  s+e++ e+ersacPt+gsCsG+ftansm+clte
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 146 GPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEKVAEYERSACPTCGSCSGMFTANSMNCLTE 207
                                                    *********8..557899********************************************** PP

                                      TIGR00110 194 alGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltkeafenaitldl 250
                                                    alGl+lPg++++lat++++++l+ ++g++ivel+k+++        Pr+i++ +afena+tld+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 208 ALGLALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGendesvlPRNIANFKAFENAMTLDI 271
                                                    **************************************99999********************* PP

                                      TIGR00110 251 alGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlk 313
                                                    a+GGstnt+Lhlla+a+ea+++++l d+drlsr+vP+l+k++P+ +k+ +ed+hraGG+ ++l+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 272 AMGGSTNTILHLLAAAQEAEIDFDLRDIDRLSRHVPQLCKVAPNIQKYhMEDVHRAGGIFSILG 335
                                                    *********************************************9999*************** PP

                                      TIGR00110 314 eldkegllhkdaltvtGktlaetlekvkvlr................................. 344
                                                    +l + gllh+d  tv  kt+ae ++k ++++                                 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 336 SLARGGLLHTDLPTVHSKTMAEAIAKWDITQttdeavhhffkagpagiptqtafsqstrwetld 399
                                                    *****************************999******************************77 PP

                                      TIGR00110 345 ..vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeai 406
                                                       ++ +irs++++++kegglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +i
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 400 ddRENGCIRSVEHAYSKEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGI 463
                                                    555555********************************************************** PP

                                      TIGR00110 407 lggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvs 470
                                                    l+ +vk+Gd+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh s
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 464 LADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHAS 527
                                                    **************************************************************** PP

                                      TIGR00110 471 PeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLak 527
                                                    Peaa+gGai+lv+dGDk+ iDi+nr ++l +s+eela rr ++++k++       r+v  aL++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 528 PEAAAGGAIGLVRDGDKVLIDIPNRSINLLISDEELAGRRVEQDNKGWkpvevrpRKVTTALKA 591
                                                    ***********************************************999***9999******* PP

                                      TIGR00110 528 yaklvssadkGavld 542
                                                    ya l++sadkGav++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 592 YALLATSADKGAVRN 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.78
//
[ok]

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:

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, or view the source code, or see 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