Alignments for a candidate for leuC in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate Echvi_2059 Echvi_2059 3-isopropylmalate dehydratase, large subunit

Query= uniprot:A0A1X9Z7T5
         (470 letters)



>FitnessBrowser__Cola:Echvi_2059
          Length = 465

 Score =  657 bits (1695), Expect = 0.0
 Identities = 318/462 (68%), Positives = 376/462 (81%)

Query: 3   KTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVATAD 62
           KTL +K+WD HVVKS  G PD+ +ID H IHEVTSP AF  L  RG  V  P++TVAT D
Sbjct: 4   KTLFDKVWDEHVVKSVPGGPDVFFIDKHFIHEVTSPVAFLNLENRGNNVLFPERTVATPD 63

Query: 63  HNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLPGK 122
           HNVPT++Q   IK++LSR QV+ L  NC+++G+EL+ LG    GIVHVIGPELGIT PG 
Sbjct: 64  HNVPTIDQDKTIKDKLSRMQVEKLRDNCSKYGIELHDLGTDHHGIVHVIGPELGITQPGM 123

Query: 123 TMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGAKD 182
           T+VCGDSHTSTHGAFGAIAFGIGTS+VE VFA+QC++QSKPK M+I VNGELGKGV +KD
Sbjct: 124 TIVCGDSHTSTHGAFGAIAFGIGTSEVEMVFASQCIMQSKPKRMRITVNGELGKGVTSKD 183

Query: 183 IILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTFDY 242
           IILYII+KISA+GGTGYFIEYAGSAI++LSMEARMTICNMSIEMGARGGLIAPD+ TFDY
Sbjct: 184 IILYIISKISASGGTGYFIEYAGSAIQSLSMEARMTICNMSIEMGARGGLIAPDEVTFDY 243

Query: 243 IKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGIQE 302
           +KG+E AP GE+WDKA+ YWK+L +D  A+FD   T+DA DI PMITYGTNPGMG+ I++
Sbjct: 244 LKGKEHAPKGEDWDKAVEYWKSLRTDEGAEFDLEYTYDAEDIEPMITYGTNPGMGIKIKD 303

Query: 303 HIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADFVK 362
            IP T       K +Y K+LDYMGF     + GK +DYVF+GSCTN RIED+R VA+FVK
Sbjct: 304 IIPTTEGMEGSNKKTYLKSLDYMGFQPGEPIKGKKIDYVFVGSCTNGRIEDIRAVAEFVK 363

Query: 363 DKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAGKY 422
            K+KADN+T WIVPGS++VE QA  EGL  I E AGF+LR+PGCSACL MN+DKIPAGKY
Sbjct: 364 GKKKADNITAWIVPGSREVESQAIEEGLVSILEEAGFKLRQPGCSACLAMNDDKIPAGKY 423

Query: 423 CVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDL 464
            VSTSNRNFEGRQG  ARTLLASPLT AA A+TG++ D R++
Sbjct: 424 AVSTSNRNFEGRQGPGARTLLASPLTVAAVAITGEVADPREV 465


Lambda     K      H
   0.317    0.135    0.399 

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: 724
Number of extensions: 15
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: 470
Length of database: 465
Length adjustment: 33
Effective length of query: 437
Effective length of database: 432
Effective search space:   188784
Effective search space used:   188784
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 Echvi_2059 Echvi_2059 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.271852.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.4e-203  661.8   0.1   2.9e-203  661.6   0.1    1.0  1  FitnessBrowser__Cola:Echvi_2059  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Cola:Echvi_2059  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  661.6   0.1  2.9e-203  2.9e-203       2     466 .]       3     465 .]       2     465 .] 0.99

  Alignments for each domain:
  == domain 1  score: 661.6 bits;  conditional E-value: 2.9e-203
                        TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeeka 79 
                                       ktl++k++d+hvvk   +++d+++id+h++hevtsp af  l+++g +v  +++t+at dhn++t  +d +ik++ +
  FitnessBrowser__Cola:Echvi_2059   3 KKTLFDKVWDEHVVKSVPGGPDVFFIDKHFIHEVTSPVAFLNLENRGNNVLFPERTVATPDHNVPTIDQDKTIKDKLS 80 
                                      59**************************************************************************** PP

                        TIGR00170  80 klqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlatqt 157
                                      ++qv++l  n+ ++g++l+dl + + givhv+gpe g+t pg+tivcgdsht+thgafga+afgigtseve v+a+q 
  FitnessBrowser__Cola:Echvi_2059  81 RMQVEKLRDNCSKYGIELHDLGTDHHGIVHVIGPELGITQPGMTIVCGDSHTSTHGAFGAIAFGIGTSEVEMVFASQC 158
                                      ****************************************************************************** PP

                        TIGR00170 158 lkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliap 235
                                      ++q+++k ++i+v+g+l kg+t+kdiil+ii ki+++ggtgy +e+ag ai++lsme+rmt+cnm+ie+ga+ gliap
  FitnessBrowser__Cola:Echvi_2059 159 IMQSKPKRMRITVNGELGKGVTSKDIILYIISKISASGGTGYFIEYAGSAIQSLSMEARMTICNMSIEMGARGGLIAP 236
                                      ****************************************************************************** PP

                        TIGR00170 236 dettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladp 313
                                      de+tf+y+k++++apkg++++kav+ywk+l+tdega+fd + t +a+di p++t+gtnpg+ + +++ +p  + +   
  FitnessBrowser__Cola:Echvi_2059 237 DEVTFDYLKGKEHAPKGEDWDKAVEYWKSLRTDEGAEFDLEYTYDAEDIEPMITYGTNPGMGIKIKDIIPTTEGMEGS 314
                                      ***********************************************************************9999765 PP

                        TIGR00170 314 vekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekeg 391
                                       +k++  k+l+y+g++pg ++k  k+d vf+gsctn+ried+ra ae vkgkk+adn+  a +vpgs  v  qa +eg
  FitnessBrowser__Cola:Echvi_2059 315 -NKKTYLKSLDYMGFQPGEPIKGKKIDYVFVGSCTNGRIEDIRAVAEFVKGKKKADNIT-AWIVPGSREVESQAIEEG 390
                                      .677889***************************************************9.9***************** PP

                        TIGR00170 392 ldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                      l  i+ eagf+ r++gcs cl+mn+d++++++   stsnrnfegrqg gart l sp   aa a++g+ +d re+
  FitnessBrowser__Cola:Echvi_2059 391 LVSILEEAGFKLRQPGCSACLAMNDDKIPAGKYAVSTSNRNFEGRQGPGARTLLASPLTVAAVAITGEVADPREV 465
                                      ***********************************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (465 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.43
//
[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