Alignments for a candidate for ilvD in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Arcobacter nitrofigilis DSM 7299

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013136370.1 ARNIT_RS12880 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000092245.1:WP_013136370.1
          Length = 562

 Score =  496 bits (1278), Expect = e-145
 Identities = 261/561 (46%), Positives = 374/561 (66%), Gaps = 14/561 (2%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SD +K+G  RAPHRSL    GL DDDF KPFIG+ANS+ +I+PGH  L ++AE +KE 
Sbjct: 1   MRSDEVKKGYDRAPHRSLFRATGLKDDDFGKPFIGVANSFIEIIPGHFFLNKVAEIIKEE 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           + A G V FEFNT+ + DGIAM HDGM +SL SRE++A+++E++  AH LD ++ +P CD
Sbjct: 61  IRANGCVPFEFNTIGVDDGIAMGHDGMLFSLPSRELIANSIETVMNAHKLDAMIAIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLINVYEGVGTVSAGEMSEDELEE 179
           KIVPGM+M A R+D+P + V+GGPM  G  K G  +DL   +E VG    G+M+E+EL +
Sbjct: 121 KIVPGMIMGAIRVDVPTVFVSGGPMAKGHTKDGVPIDLATAFEAVGKFEKGDMTEEELTD 180

Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239
           +E  ACP   SC+G+FTAN+M  L EA+G++LPG  T  A++  + ++ R + +R+ E+ 
Sbjct: 181 IECNACPSGGSCSGMFTANSMNTLMEAMGIALPGNGTILALTPEREELYRKAARRVCEIA 240

Query: 240 QEN-----LKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDEL 294
           ++N      K + I+++ A  NA  VD+A+GGS+NT LH+ AIA E  G+N  L   + +
Sbjct: 241 KDNESREKFKLSNILNENAVRNAFAVDMAMGGSSNTVLHMLAIAKEA-GVNFELSDINAI 299

Query: 295 SRVIPHIASISPAGEHM-MLDLDRAGGIPAVLKTLE---DHINRECVTCTGRTVQENIEN 350
           S+ + HIA ISP+   + M D+++AGG+ AV+K +    + I  + +T +G T+ E I +
Sbjct: 300 SKRVSHIAKISPSLSTVHMEDINKAGGVNAVMKEMTKRGEDILLDNLTISGETLYEKIAD 359

Query: 351 VKVGHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDE 410
             +   ++I  +D+P  + GGLAIL GNLA +G+V+K   +     +  G A  F+ + E
Sbjct: 360 AYIKDTNIIHTIDNPYSNVGGLAILYGNLAEQGAVIKTAGITGARAL-TGKAVCFDGQPE 418

Query: 411 CMEAIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGT 469
            +  I GG++  GDV+VIRYEGPKGGPGM+EML PTS I GMGL ++VALITDGRFSG T
Sbjct: 419 AIAGILGGKVKAGDVVVIRYEGPKGGPGMQEMLAPTSLIMGMGLGDKVALITDGRFSGAT 478

Query: 470 RGPCVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK 529
           RG  +GHVSPEA E G +  + DGD I ID+    LEV LS  EI +R  +    ++ +K
Sbjct: 479 RGASIGHVSPEAAEGGMIGLLKDGDEIHIDVDQYILEVHLSEEEIAKRKATFTPLKKPLK 538

Query: 530 G-WLARYRKLAGSADTGAVLR 549
             WL +YR L  +A +GAVL+
Sbjct: 539 SKWLGQYRALVTNASSGAVLK 559


Lambda     K      H
   0.319    0.136    0.397 

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: 869
Number of extensions: 44
Number of successful extensions: 9
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: 549
Length of database: 562
Length adjustment: 36
Effective length of query: 513
Effective length of database: 526
Effective search space:   269838
Effective search space used:   269838
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_013136370.1 ARNIT_RS12880 (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.12183.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-229  746.8  10.3   7.9e-229  746.6  10.3    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013136370.1  ARNIT_RS12880 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013136370.1  ARNIT_RS12880 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.6  10.3  7.9e-229  7.9e-229       1     542 [.      14     559 ..      14     560 .. 0.97

  Alignments for each domain:
  == domain 1  score: 746.6 bits;  conditional E-value: 7.9e-229
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+l++atGlkd+d++kP+i+v+ns++ei+Pgh  l+++a+++keei+a+G v++efnti+v+DGiam
  lcl|NCBI__GCF_000092245.1:WP_013136370.1  14 PHRSLFRATGLKDDDFGKPFIGVANSFIEIIPGHFFLNKVAEIIKEEIRANGCVPFEFNTIGVDDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm++sLpsre+ia+s+etv++ah+lDa+++i++CDkivPGm+m+a+r+++P+++vsGGpm++g+tk
  lcl|NCBI__GCF_000092245.1:WP_013136370.1  83 GHDGMLFSLPSRELIANSIETVMNAHKLDAMIAIPNCDKIVPGMIMGAIRVDVPTVFVSGGPMAKGHTK 151
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                +  idl  +feavg+ ++g+++eeel++ie +acP+ gsCsG+ftansm++l+ea+G++lPg++t+la
  lcl|NCBI__GCF_000092245.1:WP_013136370.1 152 DGVPIDLATAFEAVGKFEKGDMTEEELTDIECNACPSGGSCSGMFTANSMNTLMEAMGIALPGNGTILA 220
                                               ********************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknik.....PrdiltkeafenaitldlalGGstntvLhllaiakeagv 271
                                                + e++el +k+++r+ e+ k n        ++il+++a+ na+++d+a+GGs+ntvLh+laiakeagv
  lcl|NCBI__GCF_000092245.1:WP_013136370.1 221 LTPEREELYRKAARRVCEIAKDNESrekfkLSNILNENAVRNAFAVDMAMGGSSNTVLHMLAIAKEAGV 289
                                               ******************99876544444499************************************* PP

                                 TIGR00110 272 klslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetle 338
                                               +++l+d++ +s++v ++ak++Ps ++v +ed+++aGGv+av+ke++k  + +  d lt++G+tl+e+++
  lcl|NCBI__GCF_000092245.1:WP_013136370.1 290 NFELSDINAISKRVSHIAKISPSLSTVhMEDINKAGGVNAVMKEMTKrGEDILLDNLTISGETLYEKIA 358
                                               ***********************99888*****************98445677788************* PP

                                 TIGR00110 339 kvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeail 407
                                               ++ ++  d+++i+++dnp+++ ggla+L+Gnlae+Gav+k+ag+       +G+a  f+ + ea+++il
  lcl|NCBI__GCF_000092245.1:WP_013136370.1 359 DAYIK--DTNIIHTIDNPYSNVGGLAILYGNLAEQGAVIKTAGITG-ARALTGKAVCFDGQPEAIAGIL 424
                                               **999..*************************************99.8899****************** PP

                                 TIGR00110 408 ggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaeg 476
                                               ggkvk+GdvvviryeGPkGgPGm+emLaPts ++g+GLg+kvaLitDGrfsG+trG siGhvsPeaaeg
  lcl|NCBI__GCF_000092245.1:WP_013136370.1 425 GGKVKAGDVVVIRYEGPKGGPGMQEMLAPTSLIMGMGLGDKVALITDGRFSGATRGASIGHVSPEAAEG 493
                                               ********************************************************************* PP

                                 TIGR00110 477 GaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               G i+l++dGD+i+iD+++  l++++seee+a+r+a+ ++ ++  ++ +L +y+ lv++a++Gavl+
  lcl|NCBI__GCF_000092245.1:WP_013136370.1 494 GMIGLLKDGDEIHIDVDQYILEVHLSEEEIAKRKATFTPLKKPLKSKWLGQYRALVTNASSGAVLK 559
                                               **************************************99999999******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (562 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: 00:00:00.02
# Mc/sec: 12.84
//
[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