Alignments for a candidate for ilvD in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Bacteroides thetaiotaomicron VPI-5482

Align dihydroxyacid dehydratase (characterized)
to candidate 351606 BT2078 dihydroxy-acid dehydratase (NCBI ptt file)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__Btheta:351606
          Length = 600

 Score =  772 bits (1993), Expect = 0.0
 Identities = 396/606 (65%), Positives = 470/606 (77%), Gaps = 15/606 (2%)

Query: 5   RSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLVAEQI 64
           RS+ +T GR MAGARALW A GM     GKPIIA+VNSFTQFVPGHVHL ++G+LV  +I
Sbjct: 6   RSSFSTQGRRMAGARALWAANGMKKNQMGKPIIAIVNSFTQFVPGHVHLHEIGQLVKAEI 65

Query: 65  EAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDK 124
           E  G  A EFNTIA+DDGIAMGH GMLYSLPSR++IADSVEYMVNAH ADAMVCISNCDK
Sbjct: 66  EKLGCFAAEFNTIAIDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHKADAMVCISNCDK 125

Query: 125 ITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQSDQV 184
           ITPGMLMA++RLNIP +FVSGGPMEAG+         LDL+DAMI+ AD  VSD +   +
Sbjct: 126 ITPGMLMAAMRLNIPTVFVSGGPMEAGEWNGQH----LDLIDAMIKSADDSVSDQEVANI 181

Query: 185 ERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIVELTK 244
           E++ACPTCG CSGMFTANSMNCL EA+GL+ PGNG+++ATH +R +LF +A K IVE   
Sbjct: 182 EQNACPTCGCCSGMFTANSMNCLNEAIGLALPGNGTIVATHENRTKLFEDAAKLIVENAM 241

Query: 245 RYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSDIDKL 304
           +YYE+ DES LPR+IA++ AF NAMTLDIAMGGSTNTVLHLLA A EA +DF M DID L
Sbjct: 242 KYYEEGDESVLPRSIATRQAFLNAMTLDIAMGGSTNTVLHLLAVAHEAGVDFKMDDIDML 301

Query: 305 SRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQTLEQY 364
           SRK P LCKVAP+TQKYH++DV+RAGG+I IL EL + GL++  V  V G++L + ++QY
Sbjct: 302 SRKTPCLCKVAPNTQKYHIQDVNRAGGIIAILAELAKGGLIDTSVLRVDGMSLAEAIDQY 361

Query: 365 DVMLTQDDAVKNMFRAGPAGIRTTQAF-SQDCRWDTLDDDRANGCIRSLEHAYSKDGGLA 423
            +             +  AG R      SQ   +  LD DRANGCIR LEHAYSKDGGLA
Sbjct: 362 SITSPNVTEKAMSKYSSAAGNRFNLVLGSQGAYYQELDKDRANGCIRDLEHAYSKDGGLA 421

Query: 424 VLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRYEGP 483
           VL GN A++GC+VKTAGVD+SI KFTGPAKV++SQ+ A E ILGG+VV+GDVVVI +EGP
Sbjct: 422 VLKGNIAQDGCVVKTAGVDESIWKFTGPAKVFDSQEAACEGILGGRVVSGDVVVITHEGP 481

Query: 484 KGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGLIED 543
           KGGPGMQEMLYPTS++KS  LGK CALITDGRFSGGTSGLSIGHVSPEAA+GG+IG I D
Sbjct: 482 KGGPGMQEMLYPTSYIKSRHLGKECALITDGRFSGGTSGLSIGHVSPEAAAGGNIGKIVD 541

Query: 544 GDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLATSA 603
           GD+I IDIP R I ++++D ELAAR            TP  R+R V  +L+AYAS+ +SA
Sbjct: 542 GDIIEIDIPARTINVRLTDEELAAR----------PMTPVTRDRYVPKSLKAYASMVSSA 591

Query: 604 DKGAVR 609
           DKGAVR
Sbjct: 592 DKGAVR 597


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: 1143
Number of extensions: 42
Number of successful extensions: 4
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: 600
Length adjustment: 37
Effective length of query: 579
Effective length of database: 563
Effective search space:   325977
Effective search space used:   325977
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 351606 BT2078 (dihydroxy-acid dehydratase (NCBI ptt file))
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.373369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   5.8e-241  786.6   9.5   6.7e-241  786.4   9.5    1.0  1  FitnessBrowser__Btheta:351606  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Btheta:351606  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  786.4   9.5  6.7e-241  6.7e-241       2     541 ..      19     597 ..      18     599 .. 0.98

  Alignments for each domain:
  == domain 1  score: 786.4 bits;  conditional E-value: 6.7e-241
                      TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysLpsr 81 
                                    aral+ a G+k+++++kPiia+vns+t++vPghvhl+++++lvk+eie+ G  a efntia++DGiamgh+Gm+ysLpsr
  FitnessBrowser__Btheta:351606  19 ARALWAANGMKKNQMGKPIIAIVNSFTQFVPGHVHLHEIGQLVKAEIEKLGCFAAEFNTIAIDDGIAMGHDGMLYSLPSR 98 
                                    79****************************************************************************** PP

                      TIGR00110  82 eiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaagkls 161
                                    +iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeag+ + ++    +d+++a+++ a++ +s
  FitnessBrowser__Btheta:351606  99 DIIADSVEYMVNAHKADAMVCISNCDKITPGMLMAAMRLNIPTVFVSGGPMEAGEWN-GQ---HLDLIDAMIKSADDSVS 174
                                    ********************************************************9.55...5677899********** PP

                      TIGR00110 162 eeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik.......Pr 234
                                    ++e+ +ie++acPt+g CsG+ftansm+cl ea+Gl+lPg++t+ at++++++l++ ++k ive  +k+++       Pr
  FitnessBrowser__Btheta:351606 175 DQEVANIEQNACPTCGCCSGMFTANSMNCLNEAIGLALPGNGTIVATHENRTKLFEDAAKLIVENAMKYYEegdesvlPR 254
                                    ******************************************************************************** PP

                      TIGR00110 235 diltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlk 313
                                    +i+t++af na+tld+a+GGstntvLhlla+a+eagv++++dd+d lsrk+P+l+k++P+++k+ i+d++raGG++a+l 
  FitnessBrowser__Btheta:351606 255 SIATRQAFLNAMTLDIAMGGSTNTVLHLLAVAHEAGVDFKMDDIDMLSRKTPCLCKVAPNTQKYhIQDVNRAGGIIAILA 334
                                    ***************************************************************99*************** PP

                      TIGR00110 314 eldkegllhkdaltvtGktlaetlekvkvlr................................vdqd....virsldnpv 357
                                    el k gl+++ +l v G++lae +++++++                                 +d+d    +ir l++++
  FitnessBrowser__Btheta:351606 335 ELAKGGLIDTSVLRVDGMSLAEAIDQYSITSpnvtekamskyssaagnrfnlvlgsqgayyqeLDKDrangCIRDLEHAY 414
                                    *****************************999*****************************9944445566********* PP

                      TIGR00110 358 kkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPt 437
                                    +k+gglavLkGn+a++G+vvk+agv+e+i+kf+Gpakvf+s+e+a e+ilgg+v  Gdvvvi +eGPkGgPGm+emL+Pt
  FitnessBrowser__Btheta:351606 415 SKDGGLAVLKGNIAQDGCVVKTAGVDESIWKFTGPAKVFDSQEAACEGILGGRVVSGDVVVITHEGPKGGPGMQEMLYPT 494
                                    ******************************************************************************** PP

                      TIGR00110 438 salvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkke 517
                                    s++++  Lgk++aLitDGrfsGgt+GlsiGhvsPeaa+gG+i+ + dGD+i+iDi++r++++++ +eela+r  + ++++
  FitnessBrowser__Btheta:351606 495 SYIKSRHLGKECALITDGRFSGGTSGLSIGHVSPEAAAGGNIGKIVDGDIIEIDIPARTINVRLTDEELAARPMTPVTRD 574
                                    ************************************************************************88888887 PP

                      TIGR00110 518 arevkgaLakyaklvssadkGavl 541
                                     r+v   L++ya++vssadkGav+
  FitnessBrowser__Btheta:351606 575 -RYVPKSLKAYASMVSSADKGAVR 597
                                    .9********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (600 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: 21.06
//
[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