GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Thermophagus xiamenensis HS1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_010526299.1 GQW_RS0101505 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_000220155.1:WP_010526299.1
          Length = 608

 Score =  798 bits (2061), Expect = 0.0
 Identities = 406/606 (66%), Positives = 481/606 (79%), Gaps = 6/606 (0%)

Query: 5   RSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLVAREI 64
           RS TTT GR MAGAR LWRA GMK+   GKP+IA+ NSFTQFVPGHVHL  +GQ +   I
Sbjct: 6   RSDTTTQGRRMAGARSLWRANGMKESQMGKPLIAIVNSFTQFVPGHVHLHHIGQEIKEII 65

Query: 65  EAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCISNCDK 124
           E  G  A EFNTIAVDDGIAMGH GMLYSLPSRDLIADSVEYMVNAH ADA++CISNCDK
Sbjct: 66  EKQGCFAAEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHRADAMICISNCDK 125

Query: 125 ITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEEVEAI 184
           ITPGMLMAAMRLNIP +FVSGGPMEAG    K    ALDL+DAMV+AADDS SDEEV A+
Sbjct: 126 ITPGMLMAAMRLNIPTIFVSGGPMEAGNSNGK----ALDLIDAMVMAADDSVSDEEVLAV 181

Query: 185 EKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVVDLCQ 244
           E+ ACPTCGSCSGMFTANSMNCL EA+GL+LPGNG+++ATH +R+ LF+EA   +V+L  
Sbjct: 182 EQNACPTCGSCSGMFTANSMNCLNEAIGLALPGNGTIVATHVNRKRLFEEAANKIVELAW 241

Query: 245 RWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRL 304
           R+Y   D + LPR IATR AF NAM+LDIAMGGSTNTVLHLLA AHE G+DF+M DID+L
Sbjct: 242 RYYRDGDDSVLPRSIATRQAFMNAMTLDIAMGGSTNTVLHLLAIAHEAGVDFTMEDIDQL 301

Query: 305 SRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEALARW 364
           SR  P L+KVAP  S  H+EDV+RAGG++ IL EL R  LID S   +  PT+ EAL   
Sbjct: 302 SRKTPVLAKVAP-NSHYHIEDVNRAGGILGILAELARHNLIDTSVGRIDYPTLAEALKEH 360

Query: 365 DIGRTN-SQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDGGLA 423
           D+   + + IA E +K+AP G       SQ A ++E DLDR+NG IR VEH +SKDGGLA
Sbjct: 361 DLRSASVTDIAKEKYKSAPAGFRNLKLGSQNAVYDEFDLDRQNGCIRDVEHAYSKDGGLA 420

Query: 424 VLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRYEGP 483
           VLFGN+A +GCIVKTAGVDESIL F GTARV+ESQD+A  GIL G+VKAG+VVVI+YEGP
Sbjct: 421 VLFGNIAKDGCIVKTAGVDESILHFEGTARVYESQDSACEGILSGEVKAGDVVVIKYEGP 480

Query: 484 KGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIALVET 543
           KGGPGMQEMLYPT+Y+KS+ LG  CAL+TDGRFSGGTSGLSIGH+SPEA  GG IALV+T
Sbjct: 481 KGGPGMQEMLYPTSYIKSRHLGKECALITDGRFSGGTSGLSIGHISPEAAAGGEIALVKT 540

Query: 544 GDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMTTNA 603
           GD I+IDIP R I +++S+  L  RR+ +L +G +A+ PL+R R ++ AL+AYA+M ++A
Sbjct: 541 GDKIIIDIPQRSINVDISEEELEKRRQQELNKGTEAFKPLSRNRYVSKALQAYASMVSSA 600

Query: 604 ARGAVR 609
            +GAVR
Sbjct: 601 DKGAVR 606


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: 1104
Number of extensions: 39
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: 617
Length of database: 608
Length adjustment: 37
Effective length of query: 580
Effective length of database: 571
Effective search space:   331180
Effective search space used:   331180
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_010526299.1 GQW_RS0101505 (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.3884990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-244  796.0   5.7   9.9e-244  795.8   5.7    1.0  1  NCBI__GCF_000220155.1:WP_010526299.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010526299.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  795.8   5.7  9.9e-244  9.9e-244       2     541 ..      19     606 ..      18     608 .] 0.98

  Alignments for each domain:
  == domain 1  score: 795.8 bits;  conditional E-value: 9.9e-244
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           ar+l++a G+k+ +++kP+ia+vns+t++vPghvhl+++++ +ke ie+ G  a efntiav+DGiamgh+Gm
  NCBI__GCF_000220155.1:WP_010526299.1  19 ARSLWRANGMKESQMGKPLIAIVNSFTQFVPGHVHLHHIGQEIKEIIEKQGCFAAEFNTIAVDDGIAMGHDGM 91 
                                           69*********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr++iaDsve++v+ah++Da+++is+CDki+PGmlmaa+rlniP+i+vsGGpmeag+ + ++    +d
  NCBI__GCF_000220155.1:WP_010526299.1  92 LYSLPSRDLIADSVEYMVNAHRADAMICISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGNSN-GK---ALD 160
                                           **************************************************************99.55...567 PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +++a++++a++ +s+ee+ ++e++acPt+gsCsG+ftansm+cl ea+Gl+lPg++t+ at+ ++k+l+++++
  NCBI__GCF_000220155.1:WP_010526299.1 161 LIDAMVMAADDSVSDEEVLAVEQNACPTCGSCSGMFTANSMNCLNEAIGLALPGNGTIVATHVNRKRLFEEAA 233
                                           7899********************************************************************* PP

                             TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                           ++ivel  ++++       Pr+i+t++af na+tld+a+GGstntvLhllaia+eagv+++++d+d+lsrk+P
  NCBI__GCF_000220155.1:WP_010526299.1 234 NKIVELAWRYYRdgddsvlPRSIATRQAFMNAMTLDIAMGGSTNTVLHLLAIAHEAGVDFTMEDIDQLSRKTP 306
                                           ***********9************************************************************* PP

                             TIGR00110 287 llaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............... 344
                                           +lak++P++++ ied++raGG+ ++l el +++l+++ +  +   tlae l++++++                
  NCBI__GCF_000220155.1:WP_010526299.1 307 VLAKVAPNSHYHIEDVNRAGGILGILAELARHNLIDTSVGRIDYPTLAEALKEHDLRSasvtdiakekyksap 379
                                           ********************************************************999************** PP

                             TIGR00110 345 .....................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396
                                                                 ++ +ir ++++++k+gglavL+Gn+a++G++vk+agv+e+il+feG+a+v+
  NCBI__GCF_000220155.1:WP_010526299.1 380 agfrnlklgsqnavydefdldRQNGCIRDVEHAYSKDGGLAVLFGNIAKDGCIVKTAGVDESILHFEGTARVY 452
                                           ****************999766666************************************************ PP

                             TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhv 469
                                           es++ a e+il+g+vk+Gdvvvi+yeGPkGgPGm+emL+Pts++++  Lgk++aLitDGrfsGgt+GlsiGh+
  NCBI__GCF_000220155.1:WP_010526299.1 453 ESQDSACEGILSGEVKAGDVVVIKYEGPKGGPGMQEMLYPTSYIKSRHLGKECALITDGRFSGGTSGLSIGHI 525
                                           ************************************************************************* PP

                             TIGR00110 470 sPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........revkgaLakyaklvs 533
                                           sPeaa+gG ialv+ GDki+iDi++r +++++seeel++rr++  +k++         r+v+ aL++ya++vs
  NCBI__GCF_000220155.1:WP_010526299.1 526 SPEAAAGGEIALVKTGDKIIIDIPQRSINVDISEEELEKRRQQELNKGTeafkplsrnRYVSKALQAYASMVS 598
                                           *******************************************99999999********************** PP

                             TIGR00110 534 sadkGavl 541
                                           sadkGav+
  NCBI__GCF_000220155.1:WP_010526299.1 599 SADKGAVR 606
                                           ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (608 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: 29.17
//
[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:

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:

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:

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:

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