Alignments for a candidate for leuC in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Ammonifex degensii KC4

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_015739103.1 ADEG_RS05570 3-isopropylmalate dehydratase large subunit

Query= curated2:Q9WYC7
         (418 letters)



>NCBI__GCF_000024605.1:WP_015739103.1
          Length = 418

 Score =  465 bits (1196), Expect = e-135
 Identities = 243/420 (57%), Positives = 299/420 (71%), Gaps = 5/420 (1%)

Query: 1   MGKTLAEKIFSEHVGRDVKAGEIVLARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAF- 59
           MG+T+AEKI S   GR V+AGEIV+ARVD  MAQDGT PL I  FR++G K+   P+   
Sbjct: 1   MGQTIAEKILSRAAGRQVQAGEIVVARVDQVMAQDGTAPLAIQVFRQMGGKKPFDPERVN 60

Query: 60  LFIDHASPSPRKELSNSQKMMREFGKEMGVKVFDAGDGISHQILAEK-YVKPGDLVAGAD 118
           L IDH++PSP + +SN  KMMREF  E G +++D GDG+ HQ++ E   V PG +V GAD
Sbjct: 61  LVIDHSAPSPTESISNLHKMMREFAWEHGCRLYDIGDGVCHQVMVESGRVGPGCVVVGAD 120

Query: 119 SHTCTAGGLGAFGTGMGSTDVAIIFGLGQNWFKVPETIKVVVNGKLQDGVYAKDIILEIA 178
           SHTCT G LGAF TG+GSTD+A     G  WFKVPETIKVV +G L  GV+AKD+IL + 
Sbjct: 121 SHTCTYGALGAFATGVGSTDLAAALISGHLWFKVPETIKVVCHGPLPPGVFAKDLILYLI 180

Query: 179 RILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMGR 238
               +DGATYKA+E+ GS I+ +++E R T++NMAVE+GAK GLM  DEKT E+LK+ G 
Sbjct: 181 GRFTADGATYKAVEYTGSAIKELSMEGRFTVANMAVEMGAKVGLMEVDEKTWEWLKEHGG 240

Query: 239 EEDFRELKADPDAVYETEIEIDATTLEPLVSLPHYVDNVRKVSEVEKEKIKIDQVFIGTC 298
            E F     DPDA Y   +E D T++ P V+ PH VDNV  + +V   KI  DQ FIGTC
Sbjct: 241 GE-FTAFSPDPDAAYAKVVEFDLTSISPQVACPHRVDNVSPIEKVAGTKI--DQAFIGTC 297

Query: 299 TNGRLQDLEIALKILEKHGKHPDVRLIVGPASRKVYMDALEKGIIKKFVELGAAVIPPGC 358
           TNGRL+DL +A +IL     HP VRL+V PASRKVY+ A+ +GI+   VE GAAV+ PGC
Sbjct: 298 TNGRLEDLRVAARILAGRKIHPRVRLVVAPASRKVYLQAMREGILATLVEAGAAVVTPGC 357

Query: 359 GPCVGIHMGVLGDGERVLSTQNRNFKGRMGNPNAEIYLASPATAAATAVTGYITDPRRFI 418
           GPCVG H GV  DGE V+ST NRNFKGRMGN  AEIYLASPAT AA+A+ G ITDPR F+
Sbjct: 358 GPCVGTHNGVPADGEVVVSTANRNFKGRMGNAKAEIYLASPATVAASAIAGEITDPRLFL 417


Lambda     K      H
   0.318    0.137    0.395 

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: 493
Number of extensions: 22
Number of successful extensions: 5
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: 418
Length of database: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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: 50 (23.9 bits)

Align candidate WP_015739103.1 ADEG_RS05570 (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.6761.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-185  601.5   1.1   3.8e-185  601.3   1.1    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015739103.1  ADEG_RS05570 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015739103.1  ADEG_RS05570 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.3   1.1  3.8e-185  3.8e-185       1     410 [.       3     414 ..       3     415 .. 0.99

  Alignments for each domain:
  == domain 1  score: 601.3 bits;  conditional E-value: 3.8e-185
                                 TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPapt 68 
                                               +t+aekils+++G++v+aGeiv+++vD+vm++Dgt+pl+i+++r++g +k +++e++ lv+Dh++P+pt
  lcl|NCBI__GCF_000024605.1:WP_015739103.1   3 QTIAEKILSRAAGRQVQAGEIVVARVDQVMAQDGTAPLAIQVFRQMGgKKPFDPERVNLVIDHSAPSPT 71 
                                               699*******************************************999******************** PP

                                 TIGR02086  69 veaaelqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatD 137
                                                 +++l+k++refa e+g + +d+g+G+chqv+ve g + pg vvvgaDsht+t+GalgafatG+G+tD
  lcl|NCBI__GCF_000024605.1:WP_015739103.1  72 ESISNLHKMMREFAWEHGCRLYDIGDGVCHQVMVESGRVGPGCVVVGADSHTCTYGALGAFATGVGSTD 140
                                               ********************************************************************* PP

                                 TIGR02086 138 valalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRl 206
                                               +a+al++G++W+kvPe+ikv+ +G l   v akD+il ++++++adgatyka+e+tg+ i++ls+++R+
  lcl|NCBI__GCF_000024605.1:WP_015739103.1 141 LAAALISGHLWFKVPETIKVVCHGPLPPGVFAKDLILYLIGRFTADGATYKAVEYTGSAIKELSMEGRF 209
                                               ********************************************************************* PP

                                 TIGR02086 207 tlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvdnv 274
                                               t++n+ave+gak gl+e de+t e+lk++ g  f  +++d+da y++ +e+dl+++ p+va+Ph+vdnv
  lcl|NCBI__GCF_000024605.1:WP_015739103.1 210 TVANMAVEMGAKVGLMEVDEKTWEWLKEHGGGeFTAFSPDPDAAYAKVVEFDLTSISPQVACPHRVDNV 278
                                               ***************************99876599********************************** PP

                                 TIGR02086 275 keveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlve 343
                                                ++e+v gt+idq+fiG+CtnGRledl++aa+il gr+ h++vrl+v+Pasrkvy +a++eG++ tlve
  lcl|NCBI__GCF_000024605.1:WP_015739103.1 279 SPIEKVAGTKIDQAFIGTCTNGRLEDLRVAARILAGRKIHPRVRLVVAPASRKVYLQAMREGILATLVE 347
                                               ********************************************************************* PP

                                 TIGR02086 344 aGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpe 410
                                               aGa+++tpgCGPC+G+h Gv adgev+vst+nRnfkGRmG+ kaeiYLasPa++a+sa++Geitdp+
  lcl|NCBI__GCF_000024605.1:WP_015739103.1 348 AGAAVVTPGCGPCVGTHNGVPADGEVVVSTANRNFKGRMGNAKAEIYLASPATVAASAIAGEITDPR 414
                                               *****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (418 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.47
//
[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