Alignments for a candidate for ilvD in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Klebsiella variicola At-22

Align dihydroxyacid dehydratase (characterized)
to candidate WP_008807979.1 KVAR_RS24840 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_000025465.1:WP_008807979.1
          Length = 616

 Score = 1187 bits (3070), Expect = 0.0
 Identities = 594/616 (96%), Positives = 610/616 (99%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV
Sbjct: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSD+IIKLDLVDAMIQGADPKVSD Q
Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDKIIKLDLVDAMIQGADPKVSDEQ 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           S+QVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRK+LFLNAGKRIV
Sbjct: 181 SNQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKELFLNAGKRIV 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           ELTKRYYEQ+D SALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD
Sbjct: 241 ELTKRYYEQDDASALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGV+GILGELDRAGLLNRDVKNVLGLTLPQT
Sbjct: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVLGILGELDRAGLLNRDVKNVLGLTLPQT 360

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           LEQYDVM+TQDDAVK MFRAGPAGIRTTQAFSQDCRWDTLDDDRA GCIRSLEHAYSKDG
Sbjct: 361 LEQYDVMVTQDDAVKKMFRAGPAGIRTTQAFSQDCRWDTLDDDRAEGCIRSLEHAYSKDG 420

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQD+AV+AILGGKVV GDVVVIRY
Sbjct: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDEAVDAILGGKVVEGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPT+FLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGG+I +
Sbjct: 481 EGPKGGPGMQEMLYPTTFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGNIAI 540

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA 600
           IEDGD+IAIDIPNRGIQLQ+SDAE+AARREAQ+ARGDKAWTPK+RERQVSFALRAYASLA
Sbjct: 541 IEDGDMIAIDIPNRGIQLQLSDAEIAARREAQEARGDKAWTPKDRERQVSFALRAYASLA 600

Query: 601 TSADKGAVRDKSKLGG 616
           TSADKGAVRDKSKLGG
Sbjct: 601 TSADKGAVRDKSKLGG 616


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: 1427
Number of extensions: 39
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: 616
Length of database: 616
Length adjustment: 37
Effective length of query: 579
Effective length of database: 579
Effective search space:   335241
Effective search space used:   335241
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 WP_008807979.1 KVAR_RS24840 (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.5986.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-276  904.4   3.6   1.4e-276  904.2   3.6    1.0  1  lcl|NCBI__GCF_000025465.1:WP_008807979.1  KVAR_RS24840 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_008807979.1  KVAR_RS24840 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  904.2   3.6  1.4e-276  1.4e-276       2     542 ..      18     610 ..      17     611 .. 0.99

  Alignments for each domain:
  == domain 1  score: 904.2 bits;  conditional E-value: 1.4e-276
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG++d+d++kPiiavvns+t++vPghvhl+dl+klv+e+ieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_000025465.1:WP_008807979.1  18 ARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLVAEQIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+i+vsGGpmeagktkl
  lcl|NCBI__GCF_000025465.1:WP_008807979.1  87 HGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKL 155
                                               ********************************************************************* PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               s+ki+++d+++a+++ a++k+s+e+++++ersacPt+gsCsG+ftansm+cltealGls+Pg+++llat
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 156 SDKIIKLDLVDAMIQGADPKVSDEQSNQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLAT 224
                                               ********************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a++kel+ ++gkrivel+k++++       Pr+i++k+afena+tld+a+GGstntvLhlla+a+ea+
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 225 HADRKELFLNAGKRIVELTKRYYEqddasalPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAE 293
                                               ********************************************************************* PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               ++++++d+d+lsrkvP+l+k++Ps++k+ +ed+hraGGv ++l+eld++gll++d+++v+G tl +tle
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 294 IDFTMSDIDKLSRKVPQLCKVAPSTQKYhMEDVHRAGGVLGILGELDRAGLLNRDVKNVLGLTLPQTLE 362
                                               ***************************99**************************************** PP

                                 TIGR00110 339 kvkvlr...............................vdqd....virsldnpvkkegglavLkGnlae 372
                                               +++v+                                +d+d    +irsl+++++k+gglavL+Gn+ae
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 363 QYDVMVtqddavkkmfragpagirttqafsqdcrwdtLDDDraegCIRSLEHAYSKDGGLAVLYGNFAE 431
                                               *****99*****************************944445566************************ PP

                                 TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441
                                               +G++vk+agv+++ilkf+Gpakv+es++ea++ailggkv eGdvvviryeGPkGgPGm+emL+Pt++l+
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 432 NGCIVKTAGVDDSILKFTGPAKVYESQDEAVDAILGGKVVEGDVVVIRYEGPKGGPGMQEMLYPTTFLK 500
                                               ********************************************************************* PP

                                 TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                               ++GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gG+ia++edGD+i+iDi+nr ++l++s++e+a+rr
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 501 SMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGNIAIIEDGDMIAIDIPNRGIQLQLSDAEIAARR 569
                                               ********************************************************************* PP

                                 TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542
                                               ++++++++         r+v++aL++ya+l++sadkGav+d
  lcl|NCBI__GCF_000025465.1:WP_008807979.1 570 EAQEARGDkawtpkdreRQVSFALRAYASLATSADKGAVRD 610
                                               *****999999****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (616 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: 00:00:00.04
# Mc/sec: 7.73
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

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

Related tools

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