GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvD in Burkholderia phytofirmans PsJN

Align dihydroxyacid dehydratase (characterized)
to candidate BPHYT_RS10100 BPHYT_RS10100 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS10100 BPHYT_RS10100
           dihydroxy-acid dehydratase
          Length = 620

 Score =  919 bits (2374), Expect = 0.0
 Identities = 463/617 (75%), Positives = 524/617 (84%), Gaps = 3/617 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS T+THGRNMAGARALWRATGM D DFGKPIIAVVNSFTQFVPGHVHLRDLG LV
Sbjct: 1   MPDYRSKTSTHGRNMAGARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLRDLGALV 60

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

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQ---IIKLDLVDAMIQGADPKVS 177
           NCDKITPGMLMA++RLNIPV+FVSGGPMEAGK K       I K+DL+DAMI+  D +VS
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKSPTDGQVIAKIDLIDAMIKAGDSRVS 180

Query: 178 DSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGK 237
           D++  ++ERSACPTCGSCSGMFTANSMNCLTEA+GL+ PGNG+++ATHA RK LF  AG+
Sbjct: 181 DAEVAEIERSACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTIVATHAWRKGLFEQAGR 240

Query: 238 RIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFT 297
            +V+L +RYY+++D S LPR+IASK AFENAM LD+AMGGSTNTVLHLLAAAQE  +DFT
Sbjct: 241 LVVDLCRRYYQEDDASVLPRSIASKQAFENAMALDVAMGGSTNTVLHLLAAAQEGGVDFT 300

Query: 298 MSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTL 357
           MSDID++SRKVP LCKVAP+T K+H+EDVHRAGG+ GILGEL RA LL+    NV   TL
Sbjct: 301 MSDIDRISRKVPCLCKVAPATDKFHIEDVHRAGGIPGILGELARAELLDLSCGNVHSGTL 360

Query: 358 PQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYS 417
              + ++DV     +  +  FRA P GI TT AFSQ+  +  LD DR  GCIRS + AYS
Sbjct: 361 GNAIAKWDVAGGAGEEAQKFFRAAPGGIPTTVAFSQEATFAALDTDRNTGCIRSKQSAYS 420

Query: 418 KDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVV 477
           KDGGLAVLYGN AE GCIVKTAGVD+S   F+G A+V+ESQDDAVEAILG KVVAGDVVV
Sbjct: 421 KDGGLAVLYGNLAEKGCIVKTAGVDESQWIFSGRARVFESQDDAVEAILGDKVVAGDVVV 480

Query: 478 IRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGS 537
           IRYEGPKGGPGMQEMLYPTS+LKS GLGK+CAL TDGRFSGG+SGL IGH SPEAA GG+
Sbjct: 481 IRYEGPKGGPGMQEMLYPTSYLKSKGLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGT 540

Query: 538 IGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYA 597
           IGL+E+GD+I IDIPNR + L VSDAELA RREA +ARGDKAW P NRER VS AL+AYA
Sbjct: 541 IGLVEEGDVIEIDIPNRKMHLVVSDAELARRREAMEARGDKAWQPANRERVVSQALQAYA 600

Query: 598 SLATSADKGAVRDKSKL 614
           +LATSAD+GAVRD S+L
Sbjct: 601 ALATSADRGAVRDLSQL 617


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: 1280
Number of extensions: 52
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: 620
Length adjustment: 37
Effective length of query: 579
Effective length of database: 583
Effective search space:   337557
Effective search space used:   337557
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 BPHYT_RS10100 BPHYT_RS10100 (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.21295.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   7.6e-254  829.2   5.3   8.8e-254  828.9   5.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS10100  BPHYT_RS10100 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS10100  BPHYT_RS10100 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  828.9   5.3  8.8e-254  8.8e-254       2     542 ..      18     613 ..      17     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 828.9 bits;  conditional E-value: 8.8e-254
                                TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgh 71 
                                              aral++atG+kd d++kPiiavvns+t++vPghvhl+dl+ lv++eieaaGgvakefntiav+DGiamgh
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100  18 ARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLRDLGALVAKEIEAAGGVAKEFNTIAVDDGIAMGH 87 
                                              79******************************************************************** PP

                                TIGR00110  72 eGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl.. 139
                                              +Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+k   
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100  88 GGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKSpt 157
                                              ******************************************************************9888 PP

                                TIGR00110 140 .sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               ++ i ++d+++a++++ ++++s++e+ eiersacPt+gsCsG+ftansm+cltea+Gl+lPg++t+ at
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 158 dGQVIAKIDLIDAMIKAGDSRVSDAEVAEIERSACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTIVAT 227
                                              78999***************************************************************** PP

                                TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagv 271
                                              +a +k l++++g+ +v+l++++++       Pr+i++k+afena++ld+a+GGstntvLhlla+a+e gv
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 228 HAWRKGLFEQAGRLVVDLCRRYYQeddasvlPRSIASKQAFENAMALDVAMGGSTNTVLHLLAAAQEGGV 297
                                              ********************************************************************** PP

                                TIGR00110 272 klslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekv 340
                                              +++++d+dr+srkvP+l+k++P+++k+ ied+hraGG++++l+el +++ll+  + +v   tl++ ++k 
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 298 DFTMSDIDRISRKVPCLCKVAPATDKFhIEDVHRAGGIPGILGELARAELLDLSCGNVHSGTLGNAIAKW 367
                                              ***************************9****************************************** PP

                                TIGR00110 341 kvlr...................................vdqd..virsldnpvkkegglavLkGnlaee 373
                                              +v                                        +  +irs++++++k+gglavL+Gnlae+
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 368 DVAGgageeaqkffraapggipttvafsqeatfaaldtdR--NtgCIRSKQSAYSKDGGLAVLYGNLAEK 435
                                              **999******************************77444..256************************* PP

                                TIGR00110 374 GavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvgl 443
                                              G++vk+agv+e+ + f G+a+vfes+++a+eailg kv +GdvvviryeGPkGgPGm+emL+Pts+l++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 436 GCIVKTAGVDESQWIFSGRARVFESQDDAVEAILGDKVVAGDVVVIRYEGPKGGPGMQEMLYPTSYLKSK 505
                                              ********************************************************************** PP

                                TIGR00110 444 GLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerraka 513
                                              GLgk++aL tDGrfsGg++Gl+iGh sPeaaegG+i+lve+GD i+iDi+nrk++l vs++ela+rr+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 506 GLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGTIGLVEEGDVIEIDIPNRKMHLVVSDAELARRREAM 575
                                              ********************************************************************** PP

                                TIGR00110 514 kkkea.........revkgaLakyaklvssadkGavld 542
                                              +++++         r v+ aL++ya l++sad+Gav+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS10100 576 EARGDkawqpanreRVVSQALQAYAALATSADRGAVRD 613
                                              **999999****9999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (620 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.99
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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 preprint 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