Alignments for a candidate for leuC in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Thermus aquaticus YT-1

Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_053767404.1 BVI061214_RS04180 3-isopropylmalate dehydratase large subunit

Query= curated2:Q9RTY9
         (434 letters)



>NCBI__GCF_001280255.1:WP_053767404.1
          Length = 417

 Score =  582 bits (1501), Expect = e-171
 Identities = 302/413 (73%), Positives = 340/413 (82%), Gaps = 6/413 (1%)

Query: 18  PQTVAEKILSQRGSAAVYAGDLAVVEVDQVMVVDSIAQSFIERMERDLGAVPKYPERVSI 77
           PQT+AEKILS +    V AG+L VVEVDQVMVVDSIA SF +R++  LGA P+YPERVSI
Sbjct: 2   PQTLAEKILSHKVGRPVEAGELLVVEVDQVMVVDSIAGSFFKRLDY-LGATPRYPERVSI 60

Query: 78  VVDHVAPASTVSVAQAQKEAREYAAKTGVRLFDVGRGICHQVLMEEKLAQPGWIVLGSDS 137
           V+DHVAPA+ + VA+AQKE RE+  + G+R+FDVGRG+CHQVL+EE LAQPGWIV+GSDS
Sbjct: 61  VIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWIVVGSDS 120

Query: 138 HSTTYGAVAAFGSGMGATDIALAAASGKTWLRVPESVKVTLTGDLRPGVTAKDVALEMIR 197
           HSTTYGAV AFG+GMGATDIALAAASG+TWLRVPESVKV   G L  GVTAKD ALEM+R
Sbjct: 121 HSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGSLPRGVTAKDAALEMVR 180

Query: 198 VLGADGATYQSVEIH---AGDRFTRGERMTLANLCVEAGAKAGLVVPGGEILTDYGYDVP 254
            L A+GATY +VEIH     +  TRGERMTLANL VEAGAKAGLVVP GEIL  Y   VP
Sbjct: 181 RLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGEILEMY--QVP 238

Query: 255 AWVYPDEGAAYAREVEIDLSALHPRMSAPSEVDNVHDVAELRGLKVDQVFIGTCTNGRIE 314
            W+YPD  A Y   VEIDLS+L PR+S P  VDNVH+VAE+RG +VDQVFIGTCTNGRIE
Sbjct: 239 DWLYPDPDARYREVVEIDLSSLTPRVSVPFYVDNVHEVAEVRGKRVDQVFIGTCTNGRIE 298

Query: 315 DLHAAAEVLRGRRVDPTTRLLVIPASSQVMEEALQDGTLLTLQRAGAVLGTPGCGPCMGR 374
           DL AAAEVL+GRRV P  RLLV+PASSQV+EEA +DGTLLTL  AGA +GTPGCGPCMGR
Sbjct: 299 DLRAAAEVLKGRRVAPGVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCGPCMGR 358

Query: 375 HQGVLAPGEVCVSTSNRNFIGRMGDKDAHIYLASPAVAAATAVMGRVALPEDV 427
           H GVLAPGEVCVSTSNRNF GRMG  DA IYLASP VAAA+AV G +A PED+
Sbjct: 359 HMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYIATPEDL 411


Lambda     K      H
   0.317    0.132    0.381 

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: 640
Number of extensions: 22
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: 434
Length of database: 417
Length adjustment: 32
Effective length of query: 402
Effective length of database: 385
Effective search space:   154770
Effective search space used:   154770
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: 51 (24.3 bits)

Align candidate WP_053767404.1 BVI061214_RS04180 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)

# 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/TIGR02086.hmm
# target sequence database:        /tmp/gapView.1640190.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02086  [M=411]
Accession:   TIGR02086
Description: IPMI_arch: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-191  622.2   0.2   2.1e-191  622.0   0.2    1.0  1  NCBI__GCF_001280255.1:WP_053767404.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767404.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  622.0   0.2  2.1e-191  2.1e-191       1     411 []       3     410 ..       3     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 622.0 bits;  conditional E-value: 2.1e-191
                             TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelgakvekkekivlvfDhvvPaptveaae 73 
                                           +tlaekils+kvG++v+aGe+++v+vD+vmv+D+++ +++k+l +lga+ +++e++++v+Dhv+Pa+++e+a+
  NCBI__GCF_001280255.1:WP_053767404.1   3 QTLAEKILSHKVGRPVEAGELLVVEVDQVMVVDSIAGSFFKRLDYLGATPRYPERVSIVIDHVAPAANLEVAK 75 
                                           69*********************************************************************** PP

                             TIGR02086  74 lqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDvalalatGk 146
                                           +qkeire++k++gi+vfdvg+G+chqvl+e+g+a+pg++vvg+Dsh+tt+Ga+gaf+tG+GatD+ala+a+G+
  NCBI__GCF_001280255.1:WP_053767404.1  76 AQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWIVVGSDSHSTTYGAVGAFGTGMGATDIALAAASGR 148
                                           ************************************************************************* PP

                             TIGR02086 147 tWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgee.iealsldeRltlsnlaveagak 218
                                           tWl+vPes+kv+++G+l   vtakD +le+v++l+a+gaty+a+e++  + +eal+ +eR+tl+nl+veagak
  NCBI__GCF_001280255.1:WP_053767404.1 149 TWLRVPESVKVVFRGSLPRGVTAKDAALEMVRRLTAEGATYMAVEIHLLDgAEALTRGERMTLANLTVEAGAK 221
                                           ***********************************************99889********************* PP

                             TIGR02086 219 aglvepdeetleylkkrrgefrilkadedakyeeeieidlseleplvavPhsvdnvkeveevegteidqvfiG 291
                                           aglv+p+ e+le  +++++++  l++d+da+y e +eidls+l+p+v+vP++vdnv+ev+ev+g+++dqvfiG
  NCBI__GCF_001280255.1:WP_053767404.1 222 AGLVVPSGEILE--MYQVPDW--LYPDPDARYREVVEIDLSSLTPRVSVPFYVDNVHEVAEVRGKRVDQVFIG 290
                                           ************..8888888..9************************************************* PP

                             TIGR02086 292 sCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlveaGaiiltpgCGPClGahlGvl 364
                                           +CtnGR+edl++aae+l+gr+v++ vrl+vvPas++v+e+a+++G++ tl+eaGa+i tpgCGPC+G+h+Gvl
  NCBI__GCF_001280255.1:WP_053767404.1 291 TCTNGRIEDLRAAAEVLKGRRVAPGVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCGPCMGRHMGVL 363
                                           ************************************************************************* PP

                             TIGR02086 365 adgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpee 411
                                           a+gev+vst+nRnf+GRmG+p+aeiYLasP+vaa+sav+G+i++pe+
  NCBI__GCF_001280255.1:WP_053767404.1 364 APGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYIATPED 410
                                           ********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (417 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.06
//
[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 2024 update 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 original 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