Alignments for a candidate for ilvD in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Herbaspirillum seropedicae SmR1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate HSERO_RS02650 HSERO_RS02650 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__HerbieS:HSERO_RS02650
          Length = 620

 Score =  908 bits (2347), Expect = 0.0
 Identities = 459/617 (74%), Positives = 518/617 (83%), Gaps = 8/617 (1%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS TTT GRNMAGAR LWRATGMKD DF KPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPTYRSYTTTQGRNMAGARALWRATGMKDGDFTKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIEAAGGVAKEFNTIAVDD    G   MLYSLPSR+LIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDSGTHGDARMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHA----LDLVDAMVAAADDKI 176
           NCDKITPGMLMA++RLNIP VFVSGGPMEAGKV+    T      LDLVDAM+ A D  I
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVIKTVNTDKKVIKLDLVDAMIQAGDKNI 180

Query: 177 SDEDVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAG 236
           SD DV  +ERSACPTCGSCSGMFTANSMNCLTE LGLSLPGNG+ +ATH DRK LF+ AG
Sbjct: 181 SDADVAEVERSACPTCGSCSGMFTANSMNCLTEVLGLSLPGNGTIVATHADRKELFLRAG 240

Query: 237 HLIVDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDF 296
            LIV+LA+R+YEQDD   LPR I +K+ +ENAMTLD++MGGSTNTVLH+LAAAHE +++F
Sbjct: 241 RLIVELAKRHYEQDDYSILPRNICTKETWENAMTLDVSMGGSTNTVLHLLAAAHEAKVEF 300

Query: 297 TMADIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAET 356
           TMADID +SRRVPCL KVAP  +  H+EDVHRAGGI+SILGEL + GLL+   PTVH++T
Sbjct: 301 TMADIDRISRRVPCLCKVAPMTNKYHIEDVHRAGGIISILGELARAGLLDTSRPTVHSKT 360

Query: 357 LGDAIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPF 416
           LG+AI+++DI  ++   V K +RAAPGG+PTQVAFSQE R++  D DR NG IR  EH +
Sbjct: 361 LGEAIEKFDIRVSSDPAVHKLFRAAPGGVPTQVAFSQEERFEANDLDRANGCIRDREHAY 420

Query: 417 SKDGGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVV 476
           S+DGGLAVL GN+A  GCIVKTAGVDESILKFSG ARVFESQDA+V+ IL ++VKAGDVV
Sbjct: 421 SQDGGLAVLYGNIAEKGCIVKTAGVDESILKFSGTARVFESQDAAVEGILGDKVKAGDVV 480

Query: 477 VIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGG 536
           ++RYEGPKGGPGMQEMLYPTSY+KSKGLGKACAL TDGRFSGG+SGL IGHASPEAA GG
Sbjct: 481 IVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALFTDGRFSGGSSGLVIGHASPEAAEGG 540

Query: 537 TIGLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKA 593
            IGLV EGDMIDIDIPNRTI+LR+S  +LA RR   +A+G   W P   R+R V+ AL+A
Sbjct: 541 AIGLVEEGDMIDIDIPNRTINLRISSDDLAKRRTAMEARGDAAWQPGN-RQRVVSQALQA 599

Query: 594 YAAFATSADRGAVRDLN 610
           YAA  TSADRGAVRDL+
Sbjct: 600 YAALTTSADRGAVRDLS 616


Lambda     K      H
   0.318    0.134    0.391 

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: 1216
Number of extensions: 46
Number of successful extensions: 3
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: 612
Length of database: 620
Length adjustment: 37
Effective length of query: 575
Effective length of database: 583
Effective search space:   335225
Effective search space used:   335225
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 HSERO_RS02650 HSERO_RS02650 (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.969161.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.1e-247  808.8   4.5   1.3e-247  808.6   4.5    1.0  1  FitnessBrowser__HerbieS:HSERO_RS02650  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS02650  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.6   4.5  1.3e-247  1.3e-247       2     542 ..      18     614 ..      17     615 .. 0.98

  Alignments for each domain:
  == domain 1  score: 808.6 bits;  conditional E-value: 1.3e-247
                              TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                            aral++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+D  + g   
  FitnessBrowser__HerbieS:HSERO_RS02650  18 ARALWRATGMKDGDFTKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDSGTHGDAR 89 
                                            79********************************************************************** PP

                              TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl....se 141
                                            m+ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+       +
  FitnessBrowser__HerbieS:HSERO_RS02650  90 MLYSLPSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVIKtvntDK 161
                                            **************************************************************9755455589 PP

                              TIGR00110 142 kidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekk 213
                                            k++++d+++a++++ ++++s++++ e+ersacPt+gsCsG+ftansm+clte+lGlslPg++t+ at+a++k
  FitnessBrowser__HerbieS:HSERO_RS02650 162 KVIKLDLVDAMIQAGDKNISDADVAEVERSACPTCGSCSGMFTANSMNCLTEVLGLSLPGNGTIVATHADRK 233
                                            9*********************************************************************** PP

                              TIGR00110 214 elakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddf 278
                                            el+ ++g+ ivel k++++       Pr+i tke++ena+tld+ +GGstntvLhlla+a+ea+v++++ d+
  FitnessBrowser__HerbieS:HSERO_RS02650 234 ELFLRAGRLIVELAKRHYEqddysilPRNICTKETWENAMTLDVSMGGSTNTVLHLLAAAHEAKVEFTMADI 305
                                            ******************99**************************************************** PP

                              TIGR00110 279 drlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr..... 344
                                            dr+sr+vP+l+k++P ++k+ ied+hraGG++++l+el ++gll++   tv  ktl+e +ek +++      
  FitnessBrowser__HerbieS:HSERO_RS02650 306 DRISRRVPCLCKVAPMTNKYhIEDVHRAGGIISILGELARAGLLDTSRPTVHSKTLGEAIEKFDIRVssdpa 377
                                            ******************999********************************************999**** PP

                              TIGR00110 345 ..............................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedi 386
                                                                            + +ir  +++++++gglavL+Gn+ae+G++vk+agv+e+i
  FitnessBrowser__HerbieS:HSERO_RS02650 378 vhklfraapggvptqvafsqeerfeandldRANGCIRDREHAYSQDGGLAVLYGNIAEKGCIVKTAGVDESI 449
                                            ************************9977555555************************************** PP

                              TIGR00110 387 lkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfs 458
                                            lkf G+a+vfes+++a+e+ilg kvk+Gdvv++ryeGPkGgPGm+emL+Pts++++ GLgk++aL tDGrfs
  FitnessBrowser__HerbieS:HSERO_RS02650 450 LKFSGTARVFESQDAAVEGILGDKVKAGDVVIVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALFTDGRFS 521
                                            ************************************************************************ PP

                              TIGR00110 459 GgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........rev 521
                                            Gg++Gl+iGh sPeaaegGai+lve+GD+i iDi+nr+++l++s ++la+rr +++++++         r v
  FitnessBrowser__HerbieS:HSERO_RS02650 522 GGSSGLVIGHASPEAAEGGAIGLVEEGDMIDIDIPNRTINLRISSDDLAKRRTAMEARGDaawqpgnrqRVV 593
                                            **********************************************************99999****9999* PP

                              TIGR00110 522 kgaLakyaklvssadkGavld 542
                                            + aL++ya l +sad+Gav+d
  FitnessBrowser__HerbieS:HSERO_RS02650 594 SQALQAYAALTTSADRGAVRD 614
                                            *******************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 20.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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