Alignments for a candidate for ilvD in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Polaromonas naphthalenivorans CJ2

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_011802252.1 PNAP_RS14365 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_000015505.1:WP_011802252.1
          Length = 564

 Score =  873 bits (2255), Expect = 0.0
 Identities = 421/557 (75%), Positives = 492/557 (88%)

Query: 1   MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60
           +A N+RS NIT+G +R+PNRSMYYA+GY++ DF KPM+G+ANGHSTITPCN+GLQ+LADA
Sbjct: 6   IAINRRSANITEGKSRAPNRSMYYAMGYEESDFKKPMIGVANGHSTITPCNSGLQKLADA 65

Query: 61  AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120
           AIDAI+ +  N QVFGTPTISDGM+MGTEGMKYSL+SREVI+DCIET  QGQWMDGV+V+
Sbjct: 66  AIDAIEEAGGNAQVFGTPTISDGMAMGTEGMKYSLVSREVISDCIETCVQGQWMDGVLVV 125

Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180
           GGCDKNMPGG++ + R NVP I+VYGGTI PG+++GKDL IVS FEAVGE  AGRMS ED
Sbjct: 126 GGCDKNMPGGLMGMLRANVPAIFVYGGTILPGHYQGKDLNIVSVFEAVGENAAGRMSDED 185

Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240
              +E+ A P TGSCGGMYTANTMSS+FEALG+SL YSSTMANP  EK++SA ESARVL+
Sbjct: 186 LLQIERRAIPGTGSCGGMYTANTMSSAFEALGISLPYSSTMANPHDEKLNSAKESARVLI 245

Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300
           EA+K+DIKPRDI+T+KSIENAVA+IMATGGSTNAVLH+LAIAHAA VEWTIDDFER+R+K
Sbjct: 246 EAVKKDIKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAGVEWTIDDFERVRQK 305

Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360
            PV+CNLKPSGQY+A DLH+AGGIPQVMK+LL AG+LHGDC+TI+G+T+AE L +VPD P
Sbjct: 306 TPVLCNLKPSGQYLAVDLHQAGGIPQVMKMLLVAGLLHGDCITISGQTIAEVLADVPDAP 365

Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420
           RA QDVI PI++ +YA+GHLAILKGNL+ EG VAKITGLKNPV+TGPARVFEDEQS ++A
Sbjct: 366 RAGQDVIRPIDQPMYAQGHLAILKGNLSPEGCVAKITGLKNPVMTGPARVFEDEQSGLKA 425

Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480
           IL  KI AGD++VLRYLGPKGGPGMPEMLAPT A+IG GLGESVG ITDGRFSGGTWGMV
Sbjct: 426 ILDGKIVAGDVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMV 485

Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540
           VGHVAPEA  GG IA ++EGDSITIDA++LLLQLN++D EL  R+  W  PAPRYTRGV 
Sbjct: 486 VGHVAPEAAAGGNIAFIEEGDSITIDANQLLLQLNISDAELESRKVGWTAPAPRYTRGVQ 545

Query: 541 AKFSKLASTASKGAVTD 557
           AKF+  AS+ASKGAV D
Sbjct: 546 AKFAFNASSASKGAVLD 562


Lambda     K      H
   0.316    0.133    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: 1106
Number of extensions: 37
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: 557
Length of database: 564
Length adjustment: 36
Effective length of query: 521
Effective length of database: 528
Effective search space:   275088
Effective search space used:   275088
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_011802252.1 PNAP_RS14365 (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.4326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-229  747.4   5.8     5e-229  747.2   5.8    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011802252.1  PNAP_RS14365 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802252.1  PNAP_RS14365 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  747.2   5.8    5e-229    5e-229       1     542 [.      23     562 ..      23     563 .. 0.99

  Alignments for each domain:
  == domain 1  score: 747.2 bits;  conditional E-value: 5e-229
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r++++a+G+++ d++kP+i+v+n++++i+P++  l++la+++ ++ie+aGg a+ f+t ++sDG+am
  lcl|NCBI__GCF_000015505.1:WP_011802252.1  23 PNRSMYYAMGYEESDFKKPMIGVANGHSTITPCNSGLQKLADAAIDAIEEAGGNAQVFGTPTISDGMAM 91 
                                               68******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eGmkysL+sre+i+D +et v+++++D+++v++ CDk++PG lm++lr n+Pai+v+GG++ +g+++
  lcl|NCBI__GCF_000015505.1:WP_011802252.1  92 GTEGMKYSLVSREVISDCIETCVQGQWMDGVLVVGGCDKNMPGGLMGMLRANVPAIFVYGGTILPGHYQ 160
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++++++v+vfeavge aag++s+e+l +ier a P++gsC+G++tan+m++++ealG+slP+sst++ 
  lcl|NCBI__GCF_000015505.1:WP_011802252.1 161 -GKDLNIVSVFEAVGENAAGRMSDEDLLQIERRAIPGTGSCGGMYTANTMSSAFEALGISLPYSSTMAN 228
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                + ek+++ak+s++ ++e+vkk+ikPrdi+tk+++ena+++++a+GGstn+vLh laia+ agv+ ++d
  lcl|NCBI__GCF_000015505.1:WP_011802252.1 229 PHDEKLNSAKESARVLIEAVKKDIKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAGVEWTID 297
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344
                                               df+r+++k+P+l++lkPsg+++ +dlh+aGG+++v+k+l  +gllh d++t++G+t+ae+l++v+  + 
  lcl|NCBI__GCF_000015505.1:WP_011802252.1 298 DFERVRQKTPVLCNLKPSGQYLAVDLHQAGGIPQVMKMLLVAGLLHGDCITISGQTIAEVLADVPDAPr 366
                                               ***************************************************************988753 PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                               ++qdvir++d+p++++g+la+LkGnl++eG+v+ki+g ++   +++Gpa+vfe+e+  l+ail+gk+ +
  lcl|NCBI__GCF_000015505.1:WP_011802252.1 367 AGQDVIRPIDQPMYAQGHLAILKGNLSPEGCVAKITGLKN--PVMTGPARVFEDEQSGLKAILDGKIVA 433
                                               89**************************************..889************************ PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               Gdv+v+ry GPkGgPGm+emLaPt al+g+GLg++v+LitDGrfsGgt G+++Ghv+Peaa+gG+ia++
  lcl|NCBI__GCF_000015505.1:WP_011802252.1 434 GDVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGHVAPEAAAGGNIAFI 502
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               e+GD i+iD+++  l+l++s++el++r+  ++++ +r+++g+ ak+a  +ssa+kGavld
  lcl|NCBI__GCF_000015505.1:WP_011802252.1 503 EEGDSITIDANQLLLQLNISDAELESRKVGWTAPAPRYTRGVQAKFAFNASSASKGAVLD 562
                                               **********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (564 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.92
//
[ok]

This GapMind analysis is from Apr 10 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