Alignments for a candidate for leuA in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Thermocrinis albus DSM 14484

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_012992063.1 THAL_RS05225 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000025605.1:WP_012992063.1
          Length = 519

 Score =  515 bits (1326), Expect = e-150
 Identities = 272/518 (52%), Positives = 365/518 (70%), Gaps = 7/518 (1%)

Query: 6   RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIAK 65
           +V IFDTTLRDGEQ+PG +MT EEK+++A QL +LGVD++EAGFAAAS GD+EAV  IA+
Sbjct: 3   KVYIFDTTLRDGEQAPGFSMTSEEKLQMALQLARLGVDVLEAGFAAASKGDYEAVKLIAQ 62

Query: 66  TITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAAV 125
            +    +CSL+RA+E+DI  A EA+APA +KRIHTFIATS IHM YKL+M P+ V+E A 
Sbjct: 63  EVKGPVICSLARALEKDIDLAAEALAPAERKRIHTFIATSEIHMRYKLRMSPQDVLERAK 122

Query: 126 KAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEEF 185
           +AV  AR YTDDVEFSCEDA RS+ +FL  +    I+AGAT INIPDTVGYS+P +  + 
Sbjct: 123 RAVSYARRYTDDVEFSCEDATRSQREFLYRVIEEAIKAGATVINIPDTVGYSVPEEFAQL 182

Query: 186 FRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVEE 245
             ++    PN  KV+ S HCH+DLGLAVANSL A+K GARQVECT+NG+GERAGNA++EE
Sbjct: 183 IEDIRNNVPNIDKVIISVHCHDDLGLAVANSLMAVKHGARQVECTINGIGERAGNAALEE 242

Query: 246 IVMALKVRHDLFG-LETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304
           +VMALKVR D FG L T I+T +I  +S+L+  ITG  VQPNKAIVG NAFSHESGIHQ 
Sbjct: 243 VVMALKVRKDFFGDLYTSINTKEIYKTSRLLCRITGSFVQPNKAIVGDNAFSHESGIHQH 302

Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364
           GVL +  TYEIM+ E VG+ ++R+ LGK SGR+A K KL  +GIE+ SE  L   F +FK
Sbjct: 303 GVLSNPLTYEIMNPEDVGFPSSRIILGKHSGRHALKKKLQQMGIEV-SEAELERIFEKFK 361

Query: 365 ELADKKREIFDEDLHALVSDEMGSM-NAESYKFISQKISTETGEEPRADIVFSIKGEEKR 423
           ELADKK+EI+DEDL ALV +E+  + + +    +  ++ T     P A +V    G+E+ 
Sbjct: 362 ELADKKKEIYDEDLEALVYEEVMKLPDDQPVSVLHYQVQTGDKLLPTATVVIRYMGQERT 421

Query: 424 ASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGA 483
           A+ATG+GPVDA+ KAI+        L  +S+ A+T  T++Q E  + +       +G+G 
Sbjct: 422 ATATGNGPVDAVIKAIQKALDLDTKLLDFSIKALTPNTDAQAEARLVIELDGVRSSGRGV 481

Query: 484 DTDVLVATAKAYLSALSKL----EFSAAKPKAQGSGTI 517
           D D++ A+   ++ A+++      +  +K + +  GT+
Sbjct: 482 DVDIIKASVVGFVDAVNRALLRKSYILSKDRIREEGTV 519


Lambda     K      H
   0.313    0.129    0.352 

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: 609
Number of extensions: 13
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: 517
Length of database: 519
Length adjustment: 35
Effective length of query: 482
Effective length of database: 484
Effective search space:   233288
Effective search space used:   233288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_012992063.1 THAL_RS05225 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.1845709.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-251  818.7   3.6   8.2e-251  818.6   3.6    1.0  1  NCBI__GCF_000025605.1:WP_012992063.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025605.1:WP_012992063.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  818.6   3.6  8.2e-251  8.2e-251       1     494 []       3     498 ..       3     498 .. 1.00

  Alignments for each domain:
  == domain 1  score: 818.6 bits;  conditional E-value: 8.2e-251
                             TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 
                                           +v+ifdttlrdGeqapg+s+t eeklq+a++l+rlgvd++eaGf+++skgd+eav+ ia+evk +++++lara
  NCBI__GCF_000025605.1:WP_012992063.1   3 KVYIFDTTLRDGEQAPGFSMTSEEKLQMALQLARLGVDVLEAGFAAASKGDYEAVKLIAQEVKGPVICSLARA 75 
                                           79*********************************************************************** PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                           +ekdid aaeal pae+krihtfiats+ih+++kl+++ ++vler+++av+ya+ ++ddvefs+eda+r+++e
  NCBI__GCF_000025605.1:WP_012992063.1  76 LEKDIDLAAEALAPAERKRIHTFIATSEIHMRYKLRMSPQDVLERAKRAVSYARRYTDDVEFSCEDATRSQRE 148
                                           ************************************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           fl+rv+e ai+aGat+iniPdtvGy +P+e+++li+++++nvPnidk+i+svhchddlGlavansl avk+Ga
  NCBI__GCF_000025605.1:WP_012992063.1 149 FLYRVIEEAIKAGATVINIPDTVGYSVPEEFAQLIEDIRNNVPNIDKVIISVHCHDDLGLAVANSLMAVKHGA 221
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdfln.vetgintkeiyrtsrlvskltgmlvqrnkaivGdnafa 291
                                           rqvectinGiGeraGnaaleevvmalkvrkdf++ ++t+intkeiy+tsrl++++tg +vq+nkaivGdnaf 
  NCBI__GCF_000025605.1:WP_012992063.1 222 RQVECTINGIGERAGNAALEEVVMALKVRKDFFGdLYTSINTKEIYKTSRLLCRITGSFVQPNKAIVGDNAFS 294
                                           *********************************989************************************* PP

                             TIGR00973 292 hesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkk 364
                                           hesGihq+Gvl+n  tyei++pe++G+ +++++lgk+sGr+alkk+l+++G++++e el+++fekfkeladkk
  NCBI__GCF_000025605.1:WP_012992063.1 295 HESGIHQHGVLSNPLTYEIMNPEDVGFPSSRIILGKHSGRHALKKKLQQMGIEVSEAELERIFEKFKELADKK 367
                                           ************************************************************************* PP

                             TIGR00973 365 kevfdedlealvleelrq.eeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaieki 436
                                           ke++dedlealv+ee+++ ++++ + + ++qvq+g++ +ptatv ++  g+e++a+atGnGpvdav+kai+k+
  NCBI__GCF_000025605.1:WP_012992063.1 368 KEIYDEDLEALVYEEVMKlPDDQPVSVLHYQVQTGDKLLPTATVVIRYMGQERTATATGNGPVDAVIKAIQKA 440
                                           ***************999889999************************************************* PP

                             TIGR00973 437 lelevklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                           l+l++kll++si+a + ++da++e+++v+el+g+++sGrgv+ di++as+  +v+a+n
  NCBI__GCF_000025605.1:WP_012992063.1 441 LDLDTKLLDFSIKALTPNTDAQAEARLVIELDGVRSSGRGVDVDIIKASVVGFVDAVN 498
                                           ********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (519 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: 00:00:00.00
# Mc/sec: 27.19
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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