Alignments for a candidate for ilvD in Novosphingobium barchaimii LL02

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Novosphingobium barchaimii LL02

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_059150469.1 V474_RS05555 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_001046635.1:WP_059150469.1
          Length = 618

 Score = 1003 bits (2594), Expect = 0.0
 Identities = 499/617 (80%), Positives = 550/617 (89%), Gaps = 1/617 (0%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRT+THGRNMAGARGLWRATGMKD DFGKPIIAV NSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAYRSRTSTHGRNMAGARGLWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIEA+GGVAKEFNTIAVDDGIAMGH GMLYSLPSRDLIADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEASGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAAMRLNIP VFVSGGPMEAGKV +KGK++ALDLVDAMV AAD+SY+DEE
Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVILKGKVQALDLVDAMVAAADESYTDEE 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
           V AIE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH+DRE LF EAGRV V
Sbjct: 181 VAAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHSDRERLFLEAGRVAV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
           D+C R+YEQED + LPR +A+  AFENAMSLDIAMGGSTNTVLHLLAAA E G+DF+MAD
Sbjct: 241 DMCHRYYEQEDDSVLPRNVASFKAFENAMSLDIAMGGSTNTVLHLLAAAAEAGVDFTMAD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSR VPCLSKVAPAKSDVHMEDVHRAGG+ AILG+LER GL+    PTVH  T+GEA
Sbjct: 301 IDRLSRKVPCLSKVAPAKSDVHMEDVHRAGGIYAILGQLERAGLLHTDLPTVHTRTLGEA 360

Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420
           + RWDI RT      +F+KAAPGG PTQ AFSQ+ARWEELDLDRENGVIRS EH FS+DG
Sbjct: 361 IDRWDISRTTEPSVEQFYKAAPGGVPTQTAFSQSARWEELDLDRENGVIRSKEHAFSQDG 420

Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480
           G+AVL+GN+A +GCIVKTAGVD+SIL F GTARV+ESQDAAV+GILGGQV AG+VVVIRY
Sbjct: 421 GIAVLYGNIARDGCIVKTAGVDDSILKFTGTARVYESQDAAVAGILGGQVGAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540
           EGP+GGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGH SPEA EGG I L
Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAEGGEIGL 540

Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLN-RKRDLTPALRAYAAM 599
           VE GD I IDIP R I L VSD +LA RR  Q ARG DAW+P++ R R ++ AL+AYAAM
Sbjct: 541 VENGDTIEIDIPGRTINLMVSDEILAHRRSQQDARGDDAWSPVHPRPRKVSAALQAYAAM 600

Query: 600 TTNAARGAVRDVSQIER 616
           TT+A+RGA+RDV+Q++R
Sbjct: 601 TTSASRGAIRDVTQLKR 617


Lambda     K      H
   0.318    0.134    0.395 

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: 1336
Number of extensions: 47
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: 617
Length of database: 618
Length adjustment: 37
Effective length of query: 580
Effective length of database: 581
Effective search space:   336980
Effective search space used:   336980
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_059150469.1 V474_RS05555 (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.2662248.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.6e-254  829.4   2.7   7.7e-254  829.1   2.7    1.0  1  NCBI__GCF_001046635.1:WP_059150469.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150469.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  829.1   2.7  7.7e-254  7.7e-254       2     542 ..      18     611 ..      17     612 .. 0.99

  Alignments for each domain:
  == domain 1  score: 829.1 bits;  conditional E-value: 7.7e-254
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eiea+Ggvakefntiav+DGiamgh+Gm
  NCBI__GCF_001046635.1:WP_059150469.1  18 ARGLWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEASGGVAKEFNTIAVDDGIAMGHDGM 90 
                                           689********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPa++vsGGpmeagk+ l  k++ +d
  NCBI__GCF_001046635.1:WP_059150469.1  91 LYSLPSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVILKGKVQALD 163
                                           ************************************************************************* PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +++a++++a++  ++ee+ +iersacPt+gsCsG+ftansm+cltealGlslPg++++lat++++++l+ ++g
  NCBI__GCF_001046635.1:WP_059150469.1 164 LVDAMVAAADESYTDEEVAAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHSDRERLFLEAG 236
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                           +  v++++++++       Pr++++ +afena++ld+a+GGstntvLhlla+a+eagv++++ d+drlsrkvP
  NCBI__GCF_001046635.1:WP_059150469.1 237 RVAVDMCHRYYEqeddsvlPRNVASFKAFENAMSLDIAMGGSTNTVLHLLAAAAEAGVDFTMADIDRLSRKVP 309
                                           ************************************************************************* PP

                             TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344
                                           +l+k++P+ + v +ed+hraGG+ a+l++l+++gllh+d  tv  +tl+e +++ ++ r              
  NCBI__GCF_001046635.1:WP_059150469.1 310 CLSKVAPAKSDVhMEDVHRAGGIYAILGQLERAGLLHTDLPTVHTRTLGEAIDRWDISRttepsveqfykaap 382
                                           ********88888********************************************999************* PP

                             TIGR00110 345 .....................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396
                                                                 ++ virs++++++++gg+avL+Gn+a +G++vk+agv+++ilkf+G+a+v+
  NCBI__GCF_001046635.1:WP_059150469.1 383 ggvptqtafsqsarweeldldRENGVIRSKEHAFSQDGGIAVLYGNIARDGCIVKTAGVDDSILKFTGTARVY 455
                                           *****************99665666************************************************ PP

                             TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhv 469
                                           es+++a+++ilgg+v +GdvvviryeGP+GgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh 
  NCBI__GCF_001046635.1:WP_059150469.1 456 ESQDAAVAGILGGQVGAGDVVVIRYEGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHA 528
                                           ************************************************************************* PP

                             TIGR00110 470 sPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea..........revkgaLakyaklv 532
                                           sPeaaegG i+lve+GD+i+iDi+ r+++l vs+e la+rr +++++++          r+v+ aL++ya + 
  NCBI__GCF_001046635.1:WP_059150469.1 529 SPEAAEGGEIGLVENGDTIEIDIPGRTINLMVSDEILAHRRSQQDARGDdawspvhprpRKVSAALQAYAAMT 601
                                           ***********************************************9999********************** PP

                             TIGR00110 533 ssadkGavld 542
                                           +sa++Ga++d
  NCBI__GCF_001046635.1:WP_059150469.1 602 TSASRGAIRD 611
                                           ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (618 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: 17.22
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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