Alignments for a candidate for ilvD in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Paraburkholderia sp. CCGE1002

Align dihydroxyacid dehydratase (characterized)
to candidate WP_013092421.1 BC1002_RS23150 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_000092885.1:WP_013092421.1
          Length = 620

 Score =  919 bits (2374), Expect = 0.0
 Identities = 464/617 (75%), Positives = 522/617 (84%), Gaps = 3/617 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS T+THGRNMAGARALWRATGM D DFGKPIIAVVNSFTQFVPGHVHLRDLG LV
Sbjct: 1   MPNYRSRTSTHGRNMAGARALWRATGMKDDDFGKPIIAVVNSFTQFVPGHVHLRDLGALV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A+QIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AKQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQ---IIKLDLVDAMIQGADPKVS 177
           NCDKITPGMLMA++RLNIPV+FVSGGPMEAGK K       I K+DL+DAMI+ ADPK+S
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKSPTDGQVIAKIDLIDAMIKAADPKIS 180

Query: 178 DSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGK 237
           D++  +VERSACPTCGSCSGMFTANSMNCLTEA+GL+ PGNG+++ATHA RK LF  AG 
Sbjct: 181 DAEVAEVERSACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTVVATHAWRKGLFEQAGS 240

Query: 238 RIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFT 297
            +V+L +RYY++ D S LPR+IA+K AFENAMTLD+AMGGSTNTVLHLLAAAQEA +DFT
Sbjct: 241 LVVDLCRRYYQEEDVSVLPRSIATKQAFENAMTLDVAMGGSTNTVLHLLAAAQEAGVDFT 300

Query: 298 MSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTL 357
           MSDID++SRKVP LCK AP T KYH+EDVHRAGG+IGILGEL RA LL+    NV   TL
Sbjct: 301 MSDIDRISRKVPCLCKAAPMTDKYHIEDVHRAGGIIGILGELARADLLDLSCGNVHSGTL 360

Query: 358 PQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYS 417
              + ++D+     +  +  FRA P GI TT AFSQ+  + TLD DR +GCIRS E+AYS
Sbjct: 361 GNAIAKWDIAGGAGEEAQKFFRAAPGGIPTTVAFSQEATYATLDTDRKSGCIRSKENAYS 420

Query: 418 KDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVV 477
           KDGGLAVLYGN AE GCIVKTAGVD+S   F+G A+V+ESQDDAVEAILG KVV GDVVV
Sbjct: 421 KDGGLAVLYGNLAEKGCIVKTAGVDESQWLFSGRARVFESQDDAVEAILGDKVVPGDVVV 480

Query: 478 IRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGS 537
           IRYEGPKGGPGMQEMLYPTS+LKS GLGK+CAL TDGRFSGG+SGL IGH SPEAA GG+
Sbjct: 481 IRYEGPKGGPGMQEMLYPTSYLKSKGLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGT 540

Query: 538 IGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYA 597
           IGL+EDGD+I IDIP R + L VS+ ELA RR A +ARG  AW P NRER VS AL+AYA
Sbjct: 541 IGLVEDGDVIEIDIPQRKMHLAVSNEELARRRAAMEARGADAWQPTNRERVVSQALQAYA 600

Query: 598 SLATSADKGAVRDKSKL 614
           +LATSAD+GAVRD S+L
Sbjct: 601 ALATSADRGAVRDISQL 617


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: 1275
Number of extensions: 46
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: 616
Length of database: 620
Length adjustment: 37
Effective length of query: 579
Effective length of database: 583
Effective search space:   337557
Effective search space used:   337557
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_013092421.1 BC1002_RS23150 (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.15736.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-256  836.5   5.4   5.2e-256  836.3   5.4    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013092421.1  BC1002_RS23150 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013092421.1  BC1002_RS23150 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  836.3   5.4  5.2e-256  5.2e-256       2     542 ..      18     613 ..      17     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 836.3 bits;  conditional E-value: 5.2e-256
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG+kd+d++kPiiavvns+t++vPghvhl+dl+ lv+++ieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_000092885.1:WP_013092421.1  18 ARALWRATGMKDDDFGKPIIAVVNSFTQFVPGHVHLRDLGALVAKQIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+k 
  lcl|NCBI__GCF_000092885.1:WP_013092421.1  87 HGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKS 155
                                               *******************************************************************98 PP

                                 TIGR00110 140 ...sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205
                                                  ++ i ++d+++a++++a++k+s++e+ e+ersacPt+gsCsG+ftansm+cltea+Gl+lPg++t+
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 156 ptdGQVIAKIDLIDAMIKAADPKISDAEVAEVERSACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTV 224
                                               8878999************************************************************** PP

                                 TIGR00110 206 latsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiak 267
                                                at+a +k l++++g  +v+l++++++       Pr+i+tk+afena+tld+a+GGstntvLhlla+a+
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 225 VATHAWRKGLFEQAGSLVVDLCRRYYQeedvsvlPRSIATKQAFENAMTLDVAMGGSTNTVLHLLAAAQ 293
                                               **************************99***************************************** PP

                                 TIGR00110 268 eagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlae 335
                                               eagv+++++d+dr+srkvP+l+k +P ++k+ ied+hraGG++++l+el +++ll+  + +v   tl++
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 294 EAGVDFTMSDIDRISRKVPCLCKAAPMTDKYhIEDVHRAGGIIGILGELARADLLDLSCGNVHSGTLGN 362
                                               *****************************999************************************* PP

                                 TIGR00110 336 tlekvkvlr...................................vdqd..virsldnpvkkegglavLk 367
                                                ++k ++                                        +  +irs++n+++k+gglavL+
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 363 AIAKWDIAGgageeaqkffraapggipttvafsqeatyatldtdR--KsgCIRSKENAYSKDGGLAVLY 429
                                               *******999******************************66444..256******************* PP

                                 TIGR00110 368 GnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaP 436
                                               Gnlae+G++vk+agv+e+ + f G+a+vfes+++a+eailg kv  GdvvviryeGPkGgPGm+emL+P
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 430 GNLAEKGCIVKTAGVDESQWLFSGRARVFESQDDAVEAILGDKVVPGDVVVIRYEGPKGGPGMQEMLYP 498
                                               ********************************************************************* PP

                                 TIGR00110 437 tsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseee 505
                                               ts+l++ GLgk++aL tDGrfsGg++Gl+iGh sPeaaegG+i+lvedGD i+iDi++rk++l+vs+ee
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 499 TSYLKSKGLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGTIGLVEDGDVIEIDIPQRKMHLAVSNEE 567
                                               ********************************************************************* PP

                                 TIGR00110 506 laerrakakkkea.........revkgaLakyaklvssadkGavld 542
                                               la+rra++++++a         r v+ aL++ya l++sad+Gav+d
  lcl|NCBI__GCF_000092885.1:WP_013092421.1 568 LARRRAAMEARGAdawqptnreRVVSQALQAYAALATSADRGAVRD 613
                                               ***********99999****999*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (620 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: 11.45
//
[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