Alignments for a candidate for ilvD in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Alicycliphilus denitrificans K601

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_013520141.1 ALIDE2_RS05530 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_000204645.1:WP_013520141.1
          Length = 618

 Score =  924 bits (2387), Expect = 0.0
 Identities = 465/617 (75%), Positives = 519/617 (84%), Gaps = 7/617 (1%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS+T+T GRNMAGAR LWRATGMKD DF KPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAYRSKTSTAGRNMAGARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR++IADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGK--VVMHGKTHA----LDLVDAMVAAADD 174
           NCDKITPGMLMA++RLNIP +FVSGGPMEAGK  + + G +      LDL+DAMV AADD
Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKAKLAVPGTSTVQFKKLDLIDAMVMAADD 180

Query: 175 KISDEDVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVE 234
           K+SD D+   ER+ACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DR++LF  
Sbjct: 181 KVSDADLAEAERNACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLFKR 240

Query: 235 AGHLIVDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEI 294
           AG  IV+LAR+YYEQ D + LPR++  K AFENAMTLDIAMGGSTNT+LH+LA A E  I
Sbjct: 241 AGRRIVELARQYYEQGDERILPRSVGFK-AFENAMTLDIAMGGSTNTILHLLAIAQEAGI 299

Query: 295 DFTMADIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHA 354
            FTM DID LSR VP L KVAP     H+EDVHRAGGIM+ILGEL++ G L+ D PTVHA
Sbjct: 300 AFTMQDIDRLSRVVPQLCKVAPNTDKYHIEDVHRAGGIMAILGELERAGRLHTDVPTVHA 359

Query: 355 ETLGDAIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEH 414
            TLG+A+ +WDITRT  E V+ FY A PGG+P+QVAFSQ ARW  LD DR  G IRS +H
Sbjct: 360 RTLGEALAQWDITRTGDEAVKTFYMAGPGGVPSQVAFSQNARWPSLDLDRAAGCIRSYDH 419

Query: 415 PFSKDGGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGD 474
            FSK+GGLAVL GN+A DGC+VKTAGV ESIL F GPA V ESQD +V+ ILA++VKAGD
Sbjct: 420 AFSKEGGLAVLTGNIARDGCVVKTAGVHESILVFEGPAHVVESQDEAVEHILADQVKAGD 479

Query: 475 VVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAAN 534
           VVV+RYEGPKGGPGMQEMLYPTSY+KSKGLGKACAL+TDGRFSGGTSGLSIGH SPEAA 
Sbjct: 480 VVVVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEAAA 539

Query: 535 GGTIGLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAY 594
           GG IGLVR GD I IDIPNRTI + VS+ ELA RRAEQDAKGW P + R R V+ ALKAY
Sbjct: 540 GGAIGLVRNGDRIRIDIPNRTIDVLVSDEELARRRAEQDAKGWKPAQPRPRKVSAALKAY 599

Query: 595 AAFATSADRGAVRDLNV 611
           A   TSAD+GAVRDL++
Sbjct: 600 AKLVTSADKGAVRDLSL 616


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: 1228
Number of extensions: 33
Number of successful extensions: 3
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: 618
Length adjustment: 37
Effective length of query: 575
Effective length of database: 581
Effective search space:   334075
Effective search space used:   334075
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_013520141.1 ALIDE2_RS05530 (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.4183.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-261  853.3   2.7   4.3e-261  853.1   2.7    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013520141.1  ALIDE2_RS05530 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013520141.1  ALIDE2_RS05530 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  853.1   2.7  4.3e-261  4.3e-261       2     542 ..      18     613 ..      17     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 853.1 bits;  conditional E-value: 4.3e-261
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar+l++atG+kded++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_000204645.1:WP_013520141.1  18 ARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               69******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+i+vsGGpmeagk kl
  lcl|NCBI__GCF_000204645.1:WP_013520141.1  87 HDGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKAKL 155
                                               ********************************************************************9 PP

                                 TIGR00110 140 ......sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgs 202
                                                     + +++++d+++a++++a++k+s+++l e er+acPt+gsCsG+ftansm+cltealGlslPg+
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 156 avpgtsTVQFKKLDLIDAMVMAADDKVSDADLAEAERNACPTCGSCSGMFTANSMNCLTEALGLSLPGN 224
                                               88987677999********************************************************** PP

                                 TIGR00110 203 stllatsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhlla 264
                                               +t+ at+a++++l+k++g+rivel +++++       Pr++   +afena+tld+a+GGstnt+Lhlla
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 225 GTVVATHADREQLFKRAGRRIVELARQYYEqgderilPRSV-GFKAFENAMTLDIAMGGSTNTILHLLA 292
                                               ******************************99999989886.579************************ PP

                                 TIGR00110 265 iakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGkt 332
                                               ia+eag+ ++++d+drlsr vP+l+k++P+++k+ ied+hraGG++a+l+el+++g lh+d+ tv  +t
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 293 IAQEAGIAFTMQDIDRLSRVVPQLCKVAPNTDKYhIEDVHRAGGIMAILGELERAGRLHTDVPTVHART 361
                                               *********************************99********************************** PP

                                 TIGR00110 333 laetlekvkvlr...................................vdqdvirsldnpvkkegglavL 366
                                               l+e l++ +++r                                       +irs d++++kegglavL
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 362 LGEALAQWDITRtgdeavktfymagpggvpsqvafsqnarwpsldldRAAGCIRSYDHAFSKEGGLAVL 430
                                               *******************************************77444445****************** PP

                                 TIGR00110 367 kGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLa 435
                                               +Gn+a +G+vvk+agv+e+il+feGpa+v es++ea+e il+ +vk+Gdvvv+ryeGPkGgPGm+emL+
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 431 TGNIARDGCVVKTAGVHESILVFEGPAHVVESQDEAVEHILADQVKAGDVVVVRYEGPKGGPGMQEMLY 499
                                               ********************************************************************* PP

                                 TIGR00110 436 PtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevsee 504
                                               Pts++++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv++GD+i+iDi+nr++d+ vs+e
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 500 PTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIGLVRNGDRIRIDIPNRTIDVLVSDE 568
                                               ********************************************************************* PP

                                 TIGR00110 505 elaerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                               ela+rra++++k++       r+v+ aL++yaklv+sadkGav+d
  lcl|NCBI__GCF_000204645.1:WP_013520141.1 569 ELARRRAEQDAKGWkpaqprpRKVSAALKAYAKLVTSADKGAVRD 613
                                               *************999***99**********************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.93
//
[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