Alignments for a candidate for ilvD in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Herbaspirillum autotrophicum IAM 14942

Align dihydroxyacid dehydratase (characterized)
to candidate WP_050462557.1 AKL27_RS09465 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_001189915.1:WP_050462557.1
          Length = 625

 Score =  924 bits (2387), Expect = 0.0
 Identities = 458/623 (73%), Positives = 527/623 (84%), Gaps = 9/623 (1%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS TTTHGRNMAGARALWRATGM D DF KPI+AVVNSFTQFVPGHVHL+DLG++V
Sbjct: 1   MPVYRSRTTTHGRNMAGARALWRATGMKDGDFEKPIVAVVNSFTQFVPGHVHLKDLGQMV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKT---------KLSDQIIKLDLVDAMIQG 171
           NCDKITPGMLMA++RLNIPV+FVSGGPMEAGK          + + +IIK+DL+DAMI+ 
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVVETVIPGQPRDNQKIIKIDLIDAMIKA 180

Query: 172 ADPKVSDSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQL 231
            D  +SD+   ++ERSACPTCGSCSGMFTANSMNCLTEALGL+ PGNG++LATHADRK+L
Sbjct: 181 GDASISDADVAEIERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGTILATHADRKEL 240

Query: 232 FLNAGKRIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQE 291
           FL AG+ IVEL KR+YEQ+D S LPR+IA+KAAFENAMTLD++MGGSTNTVLHLLAAAQE
Sbjct: 241 FLRAGRLIVELAKRHYEQDDYSVLPRSIANKAAFENAMTLDVSMGGSTNTVLHLLAAAQE 300

Query: 292 AEIDFTMSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKN 351
           AE++F M+DID++SR VP LCKVAP T KYH+EDVHRAGG+IGILGEL RAGLL+     
Sbjct: 301 AEVEFKMADIDRISRHVPCLCKVAPMTDKYHIEDVHRAGGIIGILGELARAGLLDTSRPT 360

Query: 352 VLGLTLPQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRS 411
           +   +L + +   DV  TQD AV  MF A P G+ T  AFSQ+ R+ +LD DR+ GCIR 
Sbjct: 361 IHSKSLEEAIANNDVKQTQDPAVHKMFSAAPGGVATQTAFSQEKRFASLDLDRSTGCIRD 420

Query: 412 LEHAYSKDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVV 471
             HAYS+DGGLAVLYGN A NGCIVKTAGVD+SILKFTG A+V+ESQDDAVEAILG  V 
Sbjct: 421 KAHAYSQDGGLAVLYGNLAVNGCIVKTAGVDESILKFTGKARVFESQDDAVEAILGDVVQ 480

Query: 472 AGDVVVIRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPE 531
           AGD ++IRYEGPKGGPGMQEMLYPTS++KS GLGK+CAL TDGRFSGG+SGL IGH SPE
Sbjct: 481 AGDTIIIRYEGPKGGPGMQEMLYPTSYIKSKGLGKSCALFTDGRFSGGSSGLVIGHASPE 540

Query: 532 AASGGSIGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSF 591
           AA GG+IGL+EDGD I IDIPNR + L +SD E+A RR A +A+G +AW P NR+R VS 
Sbjct: 541 AAEGGAIGLVEDGDTIEIDIPNRRVHLAISDEEMAQRRAAMEAKGKQAWKPVNRQRVVSQ 600

Query: 592 ALRAYASLATSADKGAVRDKSKL 614
           AL+AYA+LATSAD+GAVRD  +L
Sbjct: 601 ALQAYAALATSADRGAVRDIKQL 623


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: 1247
Number of extensions: 42
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: 616
Length of database: 625
Length adjustment: 37
Effective length of query: 579
Effective length of database: 588
Effective search space:   340452
Effective search space used:   340452
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_050462557.1 AKL27_RS09465 (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.17872.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-253  828.4   8.6   1.5e-253  828.2   8.6    1.0  1  lcl|NCBI__GCF_001189915.1:WP_050462557.1  AKL27_RS09465 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001189915.1:WP_050462557.1  AKL27_RS09465 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  828.2   8.6  1.5e-253  1.5e-253       2     542 ..      18     619 ..      17     620 .. 0.98

  Alignments for each domain:
  == domain 1  score: 828.2 bits;  conditional E-value: 1.5e-253
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG+kd d+ekPi+avvns+t++vPghvhlkdl+++v++eieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_001189915.1:WP_050462557.1  18 ARALWRATGMKDGDFEKPIVAVVNSFTQFVPGHVHLKDLGQMVAREIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+  
  lcl|NCBI__GCF_001189915.1:WP_050462557.1  87 HGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVVE 155
                                               ******************************************************************987 PP

                                 TIGR00110 140 .........sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlsl 199
                                                         +ki+++d+++a++++ +  +s++++ eiersacPt+gsCsG+ftansm+cltealGl+l
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 156 tvipgqprdNQKIIKIDLIDAMIKAGDASISDADVAEIERSACPTCGSCSGMFTANSMNCLTEALGLAL 224
                                               78999999999********************************************************** PP

                                 TIGR00110 200 Pgsstllatsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLh 261
                                               Pg++t+lat+a++kel+ ++g+ ivel k++++       Pr+i++k+afena+tld+ +GGstntvLh
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 225 PGNGTILATHADRKELFLRAGRLIVELAKRHYEqddysvlPRSIANKAAFENAMTLDVSMGGSTNTVLH 293
                                               ********************************************************************* PP

                                 TIGR00110 262 llaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvt 329
                                               lla+a+ea+v++++ d+dr+sr+vP+l+k++P ++k+ ied+hraGG++++l+el ++gll++   t+ 
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 294 LLAAAQEAEVEFKMADIDRISRHVPCLCKVAPMTDKYhIEDVHRAGGIIGILGELARAGLLDTSRPTIH 362
                                               ***********************************999******************************* PP

                                 TIGR00110 330 Gktlaetlekvkvlr...................................vdqd..virsldnpvkkeg 361
                                                k+l+e +++ +v++                                      +  +ir + ++++++g
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 363 SKSLEEAIANNDVKQtqdpavhkmfsaapggvatqtafsqekrfasldldR--StgCIRDKAHAYSQDG 429
                                               *************999****************************9988444..355************* PP

                                 TIGR00110 362 glavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGm 430
                                               glavL+Gnla +G++vk+agv+e+ilkf+G+a+vfes+++a+eailg  v++Gd ++iryeGPkGgPGm
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 430 GLAVLYGNLAVNGCIVKTAGVDESILKFTGKARVFESQDDAVEAILGDVVQAGDTIIIRYEGPKGGPGM 498
                                               ********************************************************************* PP

                                 TIGR00110 431 remLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldl 499
                                               +emL+Pts++++ GLgk++aL tDGrfsGg++Gl+iGh sPeaaegGai+lvedGD+i+iDi+nr+++l
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 499 QEMLYPTSYIKSKGLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGAIGLVEDGDTIEIDIPNRRVHL 567
                                               ********************************************************************* PP

                                 TIGR00110 500 evseeelaerrakakkkea.........revkgaLakyaklvssadkGavld 542
                                               ++s+ee+a+rra++++k++         r v+ aL++ya l++sad+Gav+d
  lcl|NCBI__GCF_001189915.1:WP_050462557.1 568 AISDEEMAQRRAAMEAKGKqawkpvnrqRVVSQALQAYAALATSADRGAVRD 619
                                               ***************9999999****9999********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (625 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: 00:00:00.03
# Mc/sec: 9.14
//
[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