Alignments for a candidate for leuC in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Ferroglobus placidus DSM 10642

Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_012966926.1 FERP_RS12430 3-isopropylmalate dehydratase large subunit

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_000025505.1:WP_012966926.1
          Length = 416

 Score =  648 bits (1671), Expect = 0.0
 Identities = 310/416 (74%), Positives = 369/416 (88%)

Query: 1   MGKTIAEKILSEKSKSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTHF 60
           MGKTIAEKILSEKS  DAYAGDIV+A++D+IALQDGTAPLAI+Q+ +LG EV+AA  THF
Sbjct: 1   MGKTIAEKILSEKSGKDAYAGDIVIAKVDRIALQDGTAPLAIKQVEKLGLEVKAAKITHF 60

Query: 61  FVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSH 120
           FVDHAAPSPR+ELSNDQK I EFA+KVGA+FN PGEGIIHQ+MVERYV PGDL VGADSH
Sbjct: 61  FVDHAAPSPRKELSNDQKLIKEFAEKVGAEFNKPGEGIIHQLMVERYVNPGDLIVGADSH 120

Query: 121 TCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGD 180
           TCTYG +GAF+TGMGSTD+A+A+ALGKNWFRVPESF++ ++G   KGVFAKD+IL +IG+
Sbjct: 121 TCTYGALGAFATGMGSTDIAIAMALGKNWFRVPESFKIVVEGEFQKGVFAKDLILWIIGE 180

Query: 181 LGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREG 240
           LGVDGATYKALEFHGE  + + ++ RLTIANMA+ECGAKAG+F+SDE T+KFL E GR  
Sbjct: 181 LGVDGATYKALEFHGETIDKLDMDSRLTIANMAIECGAKAGLFKSDEVTKKFLMERGRGD 240

Query: 241 DFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNGR 300
            FRE+K DEDAEYEKE+Y DVS L P+V+KPH VDN+A I EVEG +V+QV++GTCTNGR
Sbjct: 241 KFREIKPDEDAEYEKEMYFDVSDLTPIVAKPHQVDNIARIDEVEGVKVDQVFVGTCTNGR 300

Query: 301 LSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCV 360
           LSDLEV ARILKGRKV + VRL+V PASR VY++AL++G I+  ++AGG++L PGCGPCV
Sbjct: 301 LSDLEVVARILKGRKVHKDVRLLVGPASREVYMKALERGYIQEIIKAGGVILPPGCGPCV 360

Query: 361 GIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPREFL 416
           GIH GILADGEVC+STQNRNFKGRMGNPNAEI+L+SPATAAASA++G IADPR++L
Sbjct: 361 GIHLGILADGEVCLSTQNRNFKGRMGNPNAEIYLSSPATAAASAIEGKIADPRKYL 416


Lambda     K      H
   0.318    0.136    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: 616
Number of extensions: 13
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: 416
Length of database: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
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_012966926.1 FERP_RS12430 (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.7963.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-183  595.7   0.3   2.3e-183  595.5   0.3    1.0  1  lcl|NCBI__GCF_000025505.1:WP_012966926.1  FERP_RS12430 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025505.1:WP_012966926.1  FERP_RS12430 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.5   0.3  2.3e-183  2.3e-183       1     410 [.       3     413 ..       3     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 595.5 bits;  conditional E-value: 2.3e-183
                                 TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelgakvekkekivlvfDhvvPaptv 69 
                                               kt+aekilsek+Gk+  aG+iv++kvD ++++Dgt+pl+ik++++lg +v+  +    ++Dh++P+p++
  lcl|NCBI__GCF_000025505.1:WP_012966926.1   3 KTIAEKILSEKSGKDAYAGDIVIAKVDRIALQDGTAPLAIKQVEKLGLEVKAAKITHFFVDHAAPSPRK 71 
                                               699********************************************999999999999********** PP

                                 TIGR02086  70 eaaelqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDv 138
                                               e+++ qk i+efa ++g +  + geGi+hq++ve+ y++pg+++vgaDsht+t+GalgafatG+G+tD+
  lcl|NCBI__GCF_000025505.1:WP_012966926.1  72 ELSNDQKLIKEFAEKVGAEFNKPGEGIIHQLMVER-YVNPGDLIVGADSHTCTYGALGAFATGMGSTDI 139
                                               ***********************************.********************************* PP

                                 TIGR02086 139 alalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRlt 207
                                               a+a+a+Gk+W++vPes+k+++eG+ ++ v akD+il i++elg dgatyka+ef+ge+i++l++d+Rlt
  lcl|NCBI__GCF_000025505.1:WP_012966926.1 140 AIAMALGKNWFRVPESFKIVVEGEFQKGVFAKDLILWIIGELGVDGATYKALEFHGETIDKLDMDSRLT 208
                                               ********************************************************************* PP

                                 TIGR02086 208 lsnlaveagakaglvepdeetleylkkrrge..frilkadedakyeeeieidlseleplvavPhsvdnv 274
                                               ++n+a+e gakagl+++de t+++l++r +   fr++k+deda+ye+e+ +d+s+l+p va+Ph+vdn+
  lcl|NCBI__GCF_000025505.1:WP_012966926.1 209 IANMAIECGAKAGLFKSDEVTKKFLMERGRGdkFREIKPDEDAEYEKEMYFDVSDLTPIVAKPHQVDNI 277
                                               *************************99876567************************************ PP

                                 TIGR02086 275 keveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlve 343
                                                +++eveg+++dqvf+G+CtnGRl+dl+++a+il+gr+vhkdvrl+v Pasr+vy+kale+G+i+ +++
  lcl|NCBI__GCF_000025505.1:WP_012966926.1 278 ARIDEVEGVKVDQVFVGTCTNGRLSDLEVVARILKGRKVHKDVRLLVGPASREVYMKALERGYIQEIIK 346
                                               ********************************************************************* PP

                                 TIGR02086 344 aGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpe 410
                                               aG +il+pgCGPC+G hlG+ladgev++st+nRnfkGRmG+p+aeiYL+sPa+aa+sa+eG+i+dp+
  lcl|NCBI__GCF_000025505.1:WP_012966926.1 347 AGGVILPPGCGPCVGIHLGILADGEVCLSTQNRNFKGRMGNPNAEIYLSSPATAAASAIEGKIADPR 413
                                               ******************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (416 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: 7.68
//
[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