Aligments for a candidate for ilvD in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvD in Shewanella amazonensis SB2B

Align dihydroxyacid dehydratase (characterized)
to candidate 6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__SB2B:6939185
          Length = 618

 Score =  971 bits (2510), Expect = 0.0
 Identities = 484/618 (78%), Positives = 543/618 (87%), Gaps = 2/618 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           M K RSAT+T GRNMAGARALWRATG+ D DFGKPIIA+ NSFTQFVPGHVHL+D+G LV
Sbjct: 1   MAKLRSATSTEGRNMAGARALWRATGVKDTDFGKPIIAIANSFTQFVPGHVHLKDMGSLV 60

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

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA+LRLNIPV+FVSGGPMEAGKTKLSD++IKLDLVDAM+  AD ++SD+ 
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADDRISDAD 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           S+++ERSACPTCGSCSGMFTANSMNCLTEALGLS PGNGS+LATHADR++LFL AG+R++
Sbjct: 181 SEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVM 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           +L KRYY  +D S LPR+IAS  AFENAM LD+AMGGS+NTVLHLLAAAQEAE+DFTM D
Sbjct: 241 KLAKRYYGDDDASVLPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFTMDD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGL--TLP 358
           ID++SRKVP LCKVAPST KYHMEDVHRAGGV+ ILGELDRAGLL+ DV +V     TL 
Sbjct: 301 IDRISRKVPHLCKVAPSTPKYHMEDVHRAGGVMAILGELDRAGLLHTDVNHVASEDGTLK 360

Query: 359 QTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSK 418
             LE++DV+LT+D+ V   FRAGPAGI TT+AFSQ CRWDTLDDDR  GCIRS E A+S+
Sbjct: 361 SVLERFDVVLTKDEKVHEFFRAGPAGIPTTRAFSQSCRWDTLDDDRREGCIRSREFAFSQ 420

Query: 419 DGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVI 478
           +GGLAVL GN AENGCIVKTAGVD+S LKF+G A+VYESQ+DAV  ILGG+VVAGDVVVI
Sbjct: 421 EGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGGEVVAGDVVVI 480

Query: 479 RYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSI 538
           R+EGPKGGPGMQEMLYPTS+LKS GLG  CALITDGRFSGGTSGLSIGHVSPEAASGG+I
Sbjct: 481 RFEGPKGGPGMQEMLYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTI 540

Query: 539 GLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYAS 598
           GLIE+GD I IDIP R I+L VSDAEL +RR A +A+G  AW P +R R VS AL+AYA 
Sbjct: 541 GLIENGDRIDIDIPGRSIKLLVSDAELESRRAAMNAKGPLAWKPLSRVRPVSMALKAYAM 600

Query: 599 LATSADKGAVRDKSKLGG 616
           LATSADKGAVRD SKL G
Sbjct: 601 LATSADKGAVRDVSKLEG 618


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: 1274
Number of extensions: 51
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: 618
Length adjustment: 37
Effective length of query: 579
Effective length of database: 581
Effective search space:   336399
Effective search space used:   336399
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 6939185 Sama_3279 (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.22229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-257  840.5   2.2   3.3e-257  840.3   2.2    1.0  1  lcl|FitnessBrowser__SB2B:6939185  Sama_3279 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939185  Sama_3279 dihydroxy-acid dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  840.3   2.2  3.3e-257  3.3e-257       2     542 ..      18     612 ..      17     613 .. 0.98

  Alignments for each domain:
  == domain 1  score: 840.3 bits;  conditional E-value: 3.3e-257
                         TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysL 78 
                                       aral++atG+kd d++kPiia++ns+t++vPghvhlkd+++lv+ +ie+aGg+akefntiav+DGiamgh+Gm+ysL
  lcl|FitnessBrowser__SB2B:6939185  18 ARALWRATGVKDTDFGKPIIAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSL 94 
                                       79*************************************************************************** PP

                         TIGR00110  79 psreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgey 155
                                       psre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkls+k++++d+++a++++
  lcl|FitnessBrowser__SB2B:6939185  95 PSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAA 171
                                       ***************************************************************************** PP

                         TIGR00110 156 aagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik 232
                                       a++++s++++e+iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a+++el+ ++g+r+++l k+++ 
  lcl|FitnessBrowser__SB2B:6939185 172 ADDRISDADSEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVMKLAKRYYG 248
                                       ****************************************************************************9 PP

                         TIGR00110 233 .......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.ied 301
                                              Pr+i++ +afena++ld+a+GGs+ntvLhlla+a+ea+v++++dd+dr+srkvP+l+k++Ps+ k+ +ed
  lcl|FitnessBrowser__SB2B:6939185 249 dddasvlPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFTMDDIDRISRKVPHLCKVAPSTPKYhMED 325
                                       9999******************************************************************9999*** PP

                         TIGR00110 302 lhraGGvsavlkeldkegllhkdaltvtGk..tlaetlekvkvlr...............................v 345
                                       +hraGGv+a+l+eld++gllh+d+  v+ +  tl+ +le+ +v                                 +
  lcl|FitnessBrowser__SB2B:6939185 326 VHRAGGVMAILGELDRAGLLHTDVNHVASEdgTLKSVLERFDVVLtkdekvheffragpagipttrafsqscrwdtL 402
                                       *************************99875559*********99999****************************94 PP

                         TIGR00110 346 dqd....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvv 418
                                       d+d    +irs + ++++egglavL Gnlae+G++vk+agv+e+ lkf G a+v+es+e+a+++ilgg+v +Gdvvv
  lcl|FitnessBrowser__SB2B:6939185 403 DDDrregCIRSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGGEVVAGDVVV 479
                                       4444566********************************************************************** PP

                         TIGR00110 419 iryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienr 495
                                       ir+eGPkGgPGm+emL+Pts+l++ GLg ++aLitDGrfsGgt+GlsiGhvsPeaa+gG+i+l+e+GD+i iDi+ r
  lcl|FitnessBrowser__SB2B:6939185 480 IRFEGPKGGPGMQEMLYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTIGLIENGDRIDIDIPGR 556
                                       ***************************************************************************** PP

                         TIGR00110 496 kldlevseeelaerrakakkkea.........revkgaLakyaklvssadkGavld 542
                                        ++l vs++el++rra++++k++         r v+ aL++ya l++sadkGav+d
  lcl|FitnessBrowser__SB2B:6939185 557 SIKLLVSDAELESRRAAMNAKGPlawkplsrvRPVSMALKAYAMLATSADKGAVRD 612
                                       ******************************9999********************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: 12.59
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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