Alignments for a candidate for ilvD in Calditerrivibrio nitroreducens DSM 19672

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Calditerrivibrio nitroreducens DSM 19672

Align dihydroxyacid dehydratase (characterized)
to candidate WP_013450882.1 CALNI_RS03785 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_000183405.1:WP_013450882.1
          Length = 614

 Score =  865 bits (2235), Expect = 0.0
 Identities = 437/614 (71%), Positives = 503/614 (81%), Gaps = 5/614 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGK-PIIAVVNSFTQFVPGHVHLRDLGKL 59
           MPKYRSAT+T GRNMAGARALWRATG+ + DF K PIIAVVNSFTQFVPGHVHLR++GK+
Sbjct: 1   MPKYRSATSTSGRNMAGARALWRATGVKEEDFNKKPIIAVVNSFTQFVPGHVHLREIGKM 60

Query: 60  VAEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCI 119
           + E+IE AGG+AKE NTIA+DDGIAMGH GMLYSLPSRELIADSVEYM+NAHCADAMVCI
Sbjct: 61  MVEEIEKAGGIAKEMNTIAIDDGIAMGHNGMLYSLPSRELIADSVEYMINAHCADAMVCI 120

Query: 120 SNCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDS 179
           SNCDKITPGM+MA++RLNIP IFVSGGPMEAGK  L ++  K+DLVDAM+       +D 
Sbjct: 121 SNCDKITPGMMMAAMRLNIPTIFVSGGPMEAGKINLKNEFKKMDLVDAMVAAVSKDYTDE 180

Query: 180 QSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRI 239
           ++  +ERSACPTCGSCSGMFTANSMNCL EALGL+ PGNG+LLATH  RK LF  A KRI
Sbjct: 181 ETLVIERSACPTCGSCSGMFTANSMNCLAEALGLALPGNGTLLATHKLRKGLFTAAAKRI 240

Query: 240 VELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMS 299
           VEL K YYE  DES LPR+IAS   FENAMTLDIAMGGSTNTVLH+LA A EA+++FTM 
Sbjct: 241 VELCKMYYEDGDESILPRSIASFEVFENAMTLDIAMGGSTNTVLHILAIANEAKVNFTMK 300

Query: 300 DIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQ 359
           DID+LSRK P LCKVAPST KYH+EDVHRAGG+ GILGELDRAGL++ +VK V   TL  
Sbjct: 301 DIDRLSRKTPHLCKVAPSTDKYHIEDVHRAGGIFGILGELDRAGLIHNNVKTVHSNTLKD 360

Query: 360 TLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKD 419
            + ++D+    DD  K  + A P  + T + FSQD  W+ LD DR NGCIRS+E+AYSKD
Sbjct: 361 AIGKWDIR-NGDDEAKRFYSAAPGNVPTLEPFSQDKYWE-LDLDRVNGCIRSVENAYSKD 418

Query: 420 GGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIR 479
           GGLAVL+GN AE+GCIVKTAGVD+SILKF G A+V+ESQ+DAV+AIL  K+V GDVVVIR
Sbjct: 419 GGLAVLFGNIAEDGCIVKTAGVDESILKFKGRARVFESQEDAVDAILADKIVPGDVVVIR 478

Query: 480 YEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIG 539
           YEGPKGGPGMQEMLYPTS+LKS GLGKACALITDGRFSGGTSGLSIGH+SPEAA GG+I 
Sbjct: 479 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHISPEAAEGGNIA 538

Query: 540 LIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASL 599
           +IEDGD I IDIP R I L +S  E+  RRE         + PK+R+R++S AL+AYA L
Sbjct: 539 IIEDGDEIIIDIPERRIDLNLSSDEIKKRRE--KLINTIGFRPKDRKREISQALKAYALL 596

Query: 600 ATSADKGAVRDKSK 613
            TSA +GAVRD SK
Sbjct: 597 TTSAARGAVRDLSK 610


Lambda     K      H
   0.317    0.134    0.386 

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: 1178
Number of extensions: 45
Number of successful extensions: 5
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: 616
Length of database: 614
Length adjustment: 37
Effective length of query: 579
Effective length of database: 577
Effective search space:   334083
Effective search space used:   334083
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_013450882.1 CALNI_RS03785 (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.32706.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-254  831.1   3.9   2.3e-254  830.9   3.9    1.0  1  lcl|NCBI__GCF_000183405.1:WP_013450882.1  CALNI_RS03785 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013450882.1  CALNI_RS03785 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.9   3.9  2.3e-254  2.3e-254       2     542 ..      18     607 ..      17     608 .. 0.97

  Alignments for each domain:
  == domain 1  score: 830.9 bits;  conditional E-value: 2.3e-254
                                 TIGR00110   2 arallkatGlkdedle.kPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               aral++atG+k+ed++ kPiiavvns+t++vPghvhl++++k++ eeie+aGg+ake+ntia++DGiam
  lcl|NCBI__GCF_000183405.1:WP_013450882.1  18 ARALWRATGVKEEDFNkKPIIAVVNSFTQFVPGHVHLREIGKMMVEEIEKAGGIAKEMNTIAIDDGIAM 86 
                                               79*************637*************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ysLpsre+iaDsve++++ah++Da+v+is+CDki+PGm+maa+rlniP+i+vsGGpmeagk++
  lcl|NCBI__GCF_000183405.1:WP_013450882.1  87 GHNGMLYSLPSRELIADSVEYMINAHCADAMVCISNCDKITPGMMMAAMRLNIPTIFVSGGPMEAGKIN 155
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                               l ++++++d+++a++++ +++ ++ee+  iersacPt+gsCsG+ftansm+cl+ealGl+lPg++tlla
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 156 LKNEFKKMDLVDAMVAAVSKDYTDEETLVIERSACPTCGSCSGMFTANSMNCLAEALGLALPGNGTLLA 224
                                               ********************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakea 269
                                               t++ +k l++ ++krivel+k +++       Pr+i++ e fena+tld+a+GGstntvLh+laia+ea
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 225 THKLRKGLFTAAAKRIVELCKMYYEdgdesilPRSIASFEVFENAMTLDIAMGGSTNTVLHILAIANEA 293
                                               ********************************************************************* PP

                                 TIGR00110 270 gvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetl 337
                                               +v+++++d+drlsrk+P+l+k++Ps++k+ ied+hraGG+ ++l+eld++gl+h++++tv  +tl++ +
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 294 KVNFTMKDIDRLSRKTPHLCKVAPSTDKYhIEDVHRAGGIFGILGELDRAGLIHNNVKTVHSNTLKDAI 362
                                               ****************************99*************************************** PP

                                 TIGR00110 338 ekvkvlr.................................vdqdvirsldnpvkkegglavLkGnlaee 373
                                                k ++++                                   + +irs++n+++k+gglavL+Gn+ae+
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 363 GKWDIRNgddeakrfysaapgnvptlepfsqdkyweldldRVNGCIRSVENAYSKDGGLAVLFGNIAED 431
                                               ******9*************************999976544455************************* PP

                                 TIGR00110 374 GavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvg 442
                                               G++vk+agv+e+ilkf+G+a+vfes+e+a++ail+ k+  GdvvviryeGPkGgPGm+emL+Pts+l++
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 432 GCIVKTAGVDESILKFKGRARVFESQEDAVDAILADKIVPGDVVVIRYEGPKGGPGMQEMLYPTSYLKS 500
                                               ********************************************************************* PP

                                 TIGR00110 443 lGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                                GLgk++aLitDGrfsGgt+GlsiGh+sPeaaegG+ia++edGD+i+iDi++r++dl++s +e+++rr+
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 501 KGLGKACALITDGRFSGGTSGLSIGHISPEAAEGGNIAIIEDGDEIIIDIPERRIDLNLSSDEIKKRRE 569
                                               ********************************************************************9 PP

                                 TIGR00110 512 kakkkea.......revkgaLakyaklvssadkGavld 542
                                               k  +          re++ aL++ya l +sa +Gav+d
  lcl|NCBI__GCF_000183405.1:WP_013450882.1 570 KLINTIGfrpkdrkREISQALKAYALLTTSAARGAVRD 607
                                               9765433466677799********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (614 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.04
# Mc/sec: 6.91
//
[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