Alignments for a candidate for ilvD in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Sinorhizobium medicae WSM419

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate YP_001328388.1 Smed_2723 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_000017145.1:YP_001328388.1
          Length = 612

 Score = 1144 bits (2960), Expect = 0.0
 Identities = 569/612 (92%), Positives = 588/612 (96%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA+LRLNIP VFVSGGPMEAGKVV+HGKTHALDLVDAMVAAADDK+SDED
Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVLHGKTHALDLVDAMVAAADDKVSDED 180

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           VQ IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH DRKRLFVEAGHLIV
Sbjct: 181 VQIIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRKRLFVEAGHLIV 240

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           D+ARRYYEQ+D + LPR+IASKQAFENAM LDIAMGGSTNTVLHILAAA+EGEIDFTM D
Sbjct: 241 DIARRYYEQEDERVLPRSIASKQAFENAMALDIAMGGSTNTVLHILAAAYEGEIDFTMDD 300

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           ID LSR+VPCLSKVAPAK+DVHMEDVHRAGGIMSILGELDKGGL+NRDCPTVHAETLGDA
Sbjct: 301 IDRLSRKVPCLSKVAPAKADVHMEDVHRAGGIMSILGELDKGGLINRDCPTVHAETLGDA 360

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           IDRWDITRT+SETVR F+RAAPGGIPTQ AFSQ ARWDELDTDR+NGVIRSVEHPFSKDG
Sbjct: 361 IDRWDITRTSSETVRNFFRAAPGGIPTQTAFSQAARWDELDTDRQNGVIRSVEHPFSKDG 420

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVLKGN+A+DGCIVKTAGVDESILKFSGPARVFESQD++VK ILANEVKAGDVVVIRY
Sbjct: 421 GLAVLKGNIALDGCIVKTAGVDESILKFSGPARVFESQDSAVKGILANEVKAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAANGGTIGL
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAANGGTIGL 540

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           VREGDMIDIDIPNRTI LRV E ELAARR EQDAKGW P E RKR VTTALKAYAAFATS
Sbjct: 541 VREGDMIDIDIPNRTIVLRVDEAELAARRKEQDAKGWKPVEQRKRRVTTALKAYAAFATS 600

Query: 601 ADRGAVRDLNVR 612
           ADRGAVRDL  R
Sbjct: 601 ADRGAVRDLGDR 612


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: 1352
Number of extensions: 26
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: 612
Length of database: 612
Length adjustment: 37
Effective length of query: 575
Effective length of database: 575
Effective search space:   330625
Effective search space used:   330625
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 YP_001328388.1 Smed_2723 (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.5957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-259  846.4   3.5   5.4e-259  846.1   3.5    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001328388.1  Smed_2723 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001328388.1  Smed_2723 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  846.1   3.5  5.4e-259  5.4e-259       2     542 ..      18     608 ..      17     609 .. 0.99

  Alignments for each domain:
  == domain 1  score: 846.1 bits;  conditional E-value: 5.4e-259
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_000017145.1:YP_001328388.1  18 ARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               689****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniPa++vsGGpmeagk+ l
  lcl|NCBI__GCF_000017145.1:YP_001328388.1  87 HDGMLYSLPSREIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVL 155
                                               ********************************************************************* PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                                 k + +d+++a++++a++k+s+e+++ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 156 HGKTHALDLVDAMVAAADDKVSDEDVQIIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLAT 224
                                               ********************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a++k+l+ ++g+ iv++ +++++       Pr+i++k+afena++ld+a+GGstntvLh+la+a e +
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 225 HADRKRLFVEAGHLIVDIARRYYEqedervlPRSIASKQAFENAMALDIAMGGSTNTVLHILAAAYEGE 293
                                               ********************************************************************* PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               +++++dd+drlsrkvP+l+k++P+   v +ed+hraGG++++l+eldk gl+++d+ tv  +tl++ ++
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 294 IDFTMDDIDRLSRKVPCLSKVAPAKADVhMEDVHRAGGIMSILGELDKGGLINRDCPTVHAETLGDAID 362
                                               ************************98888**************************************** PP

                                 TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372
                                               + +++r                                    ++ virs+++p++k+gglavLkGn+a 
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 363 RWDITRtssetvrnffraapggiptqtafsqaarwdeldtdRQNGVIRSVEHPFSKDGGLAVLKGNIAL 431
                                               *****9*******************************77655555************************ PP

                                 TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441
                                               +G++vk+agv+e+ilkf Gpa+vfes++ a+++il+ +vk+GdvvviryeGPkGgPGm+emL+Pts+l+
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 432 DGCIVKTAGVDESILKFSGPARVFESQDSAVKGILANEVKAGDVVVIRYEGPKGGPGMQEMLYPTSYLK 500
                                               ********************************************************************* PP

                                 TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                               + GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gG+i+lv++GD+i iDi+nr++ l+v+e+ela+rr
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 501 SKGLGKACALITDGRFSGGTSGLSIGHVSPEAANGGTIGLVREGDMIDIDIPNRTIVLRVDEAELAARR 569
                                               ********************************************************************* PP

                                 TIGR00110 511 akakkkea.......revkgaLakyaklvssadkGavld 542
                                               +++++k++       r+v  aL++ya +++sad+Gav+d
  lcl|NCBI__GCF_000017145.1:YP_001328388.1 570 KEQDAKGWkpveqrkRRVTTALKAYAAFATSADRGAVRD 608
                                               *******999**9998999******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (612 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.72
//
[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