Alignments for a candidate for ilvD in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Shewanella loihica PV-4

Align dihydroxyacid dehydratase (characterized)
to candidate 5207771 Shew_0292 dihydroxy-acid dehydratase (RefSeq)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__PV4:5207771
          Length = 616

 Score =  957 bits (2475), Expect = 0.0
 Identities = 476/614 (77%), Positives = 534/614 (86%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           M K RSAT+T GRNMAGARALWRATG+ D+DFGKPI+A+ NSFTQFVPGHVHL+D+G LV
Sbjct: 1   MAKLRSATSTQGRNMAGARALWRATGVKDSDFGKPIVAIANSFTQFVPGHVHLKDMGSLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A  IE AGG+AKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADA+VCIS
Sbjct: 61  AGAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA+LRLNIPV+FVSGGPMEAGKTKLSD++IKLDLVDAM+  AD +VSD  
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADDRVSDED 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           S+++ERSACPTCGSCSGMFTANSMNCLTEALGLS PGNGSLLATH+DR++LFL AG+R++
Sbjct: 181 SEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHSDRRELFLEAGRRVM 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
            L  RYY  +DESALPRNIAS  AFENAM LDIAMGGS+NTVLHLLAAAQEA++DFTM+D
Sbjct: 241 ALANRYYRDDDESALPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEAKVDFTMAD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           ID+LSR+VP LCKVAPST KYHMEDVHRAGGV+GILGELDRAGLL+ DV +V G  L   
Sbjct: 301 IDRLSRQVPHLCKVAPSTPKYHMEDVHRAGGVMGILGELDRAGLLHTDVSHVAGENLKAV 360

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           L QYD++ TQD+AV+  + AGPAGI TT+AFSQ CRW +LD DR  GCIR+ E A+S++G
Sbjct: 361 LVQYDLVQTQDEAVQQFYAAGPAGIPTTKAFSQSCRWPSLDVDRQEGCIRTREFAFSQEG 420

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVL GN A +GCIVKTAGVD++   F G A+VYESQDDAV  ILGG+VVAGDVVVIRY
Sbjct: 421 GLAVLSGNIAADGCIVKTAGVDEANHTFVGHARVYESQDDAVAGILGGEVVAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPTS+LKS GLG +CALITDGRFSGGTSGLSIGHVSPEAA+GG+I L
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGTSCALITDGRFSGGTSGLSIGHVSPEAAAGGTIAL 540

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA 600
           +E GD I IDIP R I L VSD  L  RR+A  ARG +AW P NRER VS AL+AYA LA
Sbjct: 541 VETGDRIEIDIPARSITLAVSDEVLETRRQAMQARGKQAWKPVNRERSVSLALKAYAMLA 600

Query: 601 TSADKGAVRDKSKL 614
           TSADKGAVRD SKL
Sbjct: 601 TSADKGAVRDVSKL 614


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: 1246
Number of extensions: 39
Number of successful extensions: 1
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: 616
Length adjustment: 37
Effective length of query: 579
Effective length of database: 579
Effective search space:   335241
Effective search space used:   335241
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 5207771 Shew_0292 (dihydroxy-acid dehydratase (RefSeq))
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.13783.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-255  833.5   3.8   4.3e-255  833.3   3.8    1.0  1  lcl|FitnessBrowser__PV4:5207771  Shew_0292 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207771  Shew_0292 dihydroxy-acid dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.3   3.8  4.3e-255  4.3e-255       2     542 ..      18     610 ..      17     611 .. 0.99

  Alignments for each domain:
  == domain 1  score: 833.3 bits;  conditional E-value: 4.3e-255
                        TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysLp 79 
                                      aral++atG+kd d++kPi+a++ns+t++vPghvhlkd+++lv+ +ie+aGg+akefntiav+DGiamgh+Gm+ysLp
  lcl|FitnessBrowser__PV4:5207771  18 ARALWRATGVKDSDFGKPIVAIANSFTQFVPGHVHLKDMGSLVAGAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLP 95 
                                      79**************************************************************************** PP

                        TIGR00110  80 sreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaa 157
                                      sre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkls+k++++d+++a++++a+
  lcl|FitnessBrowser__PV4:5207771  96 SRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAAD 173
                                      ****************************************************************************** PP

                        TIGR00110 158 gklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik... 232
                                      +++s+e++e+iersacPt+gsCsG+ftansm+cltealGlslPg+++llat+++++el+ ++g+r++ l +++++   
  lcl|FitnessBrowser__PV4:5207771 174 DRVSDEDSEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHSDRRELFLEAGRRVMALANRYYRddd 251
                                      ****************************************************************************** PP

                        TIGR00110 233 ....PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhra 305
                                          Pr+i++ +afena++ld+a+GGs+ntvLhlla+a+ea+v++++ d+drlsr+vP+l+k++Ps+ k+ +ed+hra
  lcl|FitnessBrowser__PV4:5207771 252 esalPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEAKVDFTMADIDRLSRQVPHLCKVAPSTPKYhMEDVHRA 329
                                      *******************************************************************9999******* PP

                        TIGR00110 306 GGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr...................................vdqd 348
                                      GGv+++l+eld++gllh+d+  v+G+ l+ +l ++++ +                                    ++ 
  lcl|FitnessBrowser__PV4:5207771 330 GGVMGILGELDRAGLLHTDVSHVAGENLKAVLVQYDLVQtqdeavqqfyaagpagipttkafsqscrwpsldvdRQEG 407
                                      ************************************9999******************************99544455 PP

                        TIGR00110 349 virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkG 426
                                      +ir+ + ++++egglavL Gn+a +G++vk+agv+e   +f G a+v+es+++a+++ilgg+v +GdvvviryeGPkG
  lcl|FitnessBrowser__PV4:5207771 408 CIRTREFAFSQEGGLAVLSGNIAADGCIVKTAGVDEANHTFVGHARVYESQDDAVAGILGGEVVAGDVVVIRYEGPKG 485
                                      ****************************************************************************** PP

                        TIGR00110 427 gPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevsee 504
                                      gPGm+emL+Pts+l++ GLg ++aLitDGrfsGgt+GlsiGhvsPeaa+gG+ialve GD+i+iDi++r + l+vs+e
  lcl|FitnessBrowser__PV4:5207771 486 GPGMQEMLYPTSYLKSKGLGTSCALITDGRFSGGTSGLSIGHVSPEAAAGGTIALVETGDRIEIDIPARSITLAVSDE 563
                                      ****************************************************************************** PP

                        TIGR00110 505 elaerrakakkkea.........revkgaLakyaklvssadkGavld 542
                                       l++rr++++++++         r+v+ aL++ya l++sadkGav+d
  lcl|FitnessBrowser__PV4:5207771 564 VLETRRQAMQARGKqawkpvnreRSVSLALKAYAMLATSADKGAVRD 610
                                      *********99998999****9999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (616 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: 10.68
//
[ok]

This GapMind analysis is from Apr 09 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