Alignments for a candidate for ilvD in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Rhodobacter sphaeroides ATCC 17029

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011339020.1 RSPH17029_RS19210 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_000015985.1:WP_011339020.1
          Length = 612

 Score = 1003 bits (2592), Expect = 0.0
 Identities = 502/610 (82%), Positives = 547/610 (89%), Gaps = 1/610 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP +RSRT+THGRNMAGARGLWRATG+KDSDFGKPIIA+VNSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAFRSRTSTHGRNMAGARGLWRATGVKDSDFGKPIIAIVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           ARE+EAAGG+AKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREVEAAGGIAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVM-HGKTHALDLVDAMVAAADDKISDE 179
           NCDKITPGMLMA++RLNIP VFVSGGPMEAGKV +  G+T  +DL+DAMVAAAD+K+SD+
Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVTLGDGRTVKMDLIDAMVAAADEKVSDD 180

Query: 180 DVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLI 239
           D+  IE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH  RK LF+EAG   
Sbjct: 181 DLTRIEQAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAYRKELFLEAGRRA 240

Query: 240 VDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMA 299
           V+L RRYYEQ+D   LPR IA+K+AFENAM LDIAMGGSTNTVLHILAAA EG +DFTM 
Sbjct: 241 VELCRRYYEQEDEGVLPRAIATKEAFENAMALDIAMGGSTNTVLHILAAAQEGGVDFTMD 300

Query: 300 DIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGD 359
           DIDALSRRVPCL KVAP K+DVH+EDVHRAGGIMSILGELD+GGLL+RD  TVHA TLG 
Sbjct: 301 DIDALSRRVPCLCKVAPNKADVHIEDVHRAGGIMSILGELDRGGLLHRDTRTVHAPTLGA 360

Query: 360 AIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKD 419
           AID+WDI R+N+   R+ + AAPGG+PTQVAFSQ + WD LDTDRE GVIRSV  PFSKD
Sbjct: 361 AIDQWDIGRSNAPEARELFLAAPGGVPTQVAFSQSSTWDTLDTDRETGVIRSVATPFSKD 420

Query: 420 GGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIR 479
           GGLAVLKGNLA DGCIVKTAGVDESIL F+GPA+VFESQDA+V  IL   V+AGDVVVIR
Sbjct: 421 GGLAVLKGNLAPDGCIVKTAGVDESILVFAGPAKVFESQDAAVYGILNGGVQAGDVVVIR 480

Query: 480 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIG 539
           YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAA+GG IG
Sbjct: 481 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAASGGPIG 540

Query: 540 LVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFAT 599
           LVREGD I+IDIPNRTI+L V E ELAARRAEQDAKGW P   RKR V+ ALK YA FA+
Sbjct: 541 LVREGDRIEIDIPNRTITLAVPEAELAARRAEQDAKGWKPAGPRKRKVSQALKVYAQFAS 600

Query: 600 SADRGAVRDL 609
           SAD+GAVR L
Sbjct: 601 SADKGAVRVL 610


Lambda     K      H
   0.318    0.134    0.391 

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: 1298
Number of extensions: 35
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: 612
Length of database: 612
Length adjustment: 37
Effective length of query: 575
Effective length of database: 575
Effective search space:   330625
Effective search space used:   330625
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_011339020.1 RSPH17029_RS19210 (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.14251.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.9e-259  845.3   2.3   1.1e-258  845.1   2.3    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011339020.1  RSPH17029_RS19210 dihydroxy-acid


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011339020.1  RSPH17029_RS19210 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  845.1   2.3  1.1e-258  1.1e-258       2     541 ..      18     608 ..      17     610 .. 0.98

  Alignments for each domain:
  == domain 1  score: 845.1 bits;  conditional E-value: 1.1e-258
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar l++atG+kd d++kPiia+vns+t++vPghvhlkdl++lv++e+eaaGg+akefntiav+DGiamg
  lcl|NCBI__GCF_000015985.1:WP_011339020.1  18 ARGLWRATGVKDSDFGKPIIAIVNSFTQFVPGHVHLKDLGQLVAREVEAAGGIAKEFNTIAVDDGIAMG 86 
                                               689****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPa++vsGGpmeagk++l
  lcl|NCBI__GCF_000015985.1:WP_011339020.1  87 HDGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVTL 155
                                               ********************************************************************* PP

                                 TIGR00110 140 se.kidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                               ++ +  ++d+++a++++a++k+s+++l++ie+ acPt+gsCsG+ftansm+cltealGlslPg++++la
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 156 GDgRTVKMDLIDAMVAAADEKVSDDDLTRIEQAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLA 224
                                               88345679************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakea 269
                                               t+a +kel+ ++g+r vel++++++       Pr i+tkeafena++ld+a+GGstntvLh+la+a+e 
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 225 THAYRKELFLEAGRRAVELCRRYYEqedegvlPRAIATKEAFENAMALDIAMGGSTNTVLHILAAAQEG 293
                                               ********************************************************************* PP

                                 TIGR00110 270 gvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetl 337
                                               gv++++dd+d lsr+vP+l+k++P+   v ied+hraGG++++l+eld+ gllh+d+ tv   tl+  +
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 294 GVDFTMDDIDALSRRVPCLCKVAPNKADVhIEDVHRAGGIMSILGELDRGGLLHRDTRTVHAPTLGAAI 362
                                               *************************98888*************************************** PP

                                 TIGR00110 338 ekvkvlr...................................vdqd..virsldnpvkkegglavLkGn 369
                                               ++ ++ r                                      +  virs+  p++k+gglavLkGn
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 363 DQWDIGRsnapearelflaapggvptqvafsqsstwdtldtdR--EtgVIRSVATPFSKDGGLAVLKGN 429
                                               ******99******************************77444..366********************* PP

                                 TIGR00110 370 laeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                               la++G++vk+agv+e+il+f Gpakvfes+++a+ +il+g v++GdvvviryeGPkGgPGm+emL+Pts
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 430 LAPDGCIVKTAGVDESILVFAGPAKVFESQDAAVYGILNGGVQAGDVVVIRYEGPKGGPGMQEMLYPTS 498
                                               ********************************************************************* PP

                                 TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeela 507
                                               +l++ GLgk++aLitDGrfsGgt+GlsiGh sPeaa+gG+i+lv++GD+i+iDi+nr++ l+v e+ela
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 499 YLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAASGGPIGLVREGDRIEIDIPNRTITLAVPEAELA 567
                                               ********************************************************************* PP

                                 TIGR00110 508 errakakkkea.......revkgaLakyaklvssadkGavl 541
                                               +rra++++k++       r+v+ aL+ ya+++ssadkGav+
  lcl|NCBI__GCF_000015985.1:WP_011339020.1 568 ARRAEQDAKGWkpagprkRKVSQALKVYAQFASSADKGAVR 608
                                               ***********9****9999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (612 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: 12.35
//
[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