Alignments for a candidate for leuA in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Haloglycomyces albus DSM 45210

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_025273525.1 HALAL_RS19070 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>NCBI__GCF_000527155.1:WP_025273525.1
          Length = 956

 Score =  697 bits (1798), Expect = 0.0
 Identities = 358/598 (59%), Positives = 433/598 (72%), Gaps = 43/598 (7%)

Query: 45  RYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDLLVR 104
           RYRPF EE+  + L +RTWPDR+ID AP WCAVDLRDGNQALIDPM   RK+ MF  LV 
Sbjct: 10  RYRPFHEEIR-VHLPDRTWPDRIIDHAPTWCAVDLRDGNQALIDPMDLERKKTMFQTLVD 68

Query: 105 MGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGAPRA 164
           MGYKEIEVGFP+ASQTDFDFVR +IE+  IP DV+IQVLTQCR  LI+RTF++  GA +A
Sbjct: 69  MGYKEIEVGFPAASQTDFDFVRALIEEERIPADVSIQVLTQCRDHLIKRTFESLRGARQA 128

Query: 165 IVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKY-PGTQWRFEYSPESYTGT 223
           IVHFYNSTSILQR+VVF+A++  +  IATDGA  C++ AA   P T  R+EYSPES+TGT
Sbjct: 129 IVHFYNSTSILQRKVVFQADKPSITKIATDGAELCLKYAADITPDTDIRYEYSPESFTGT 188

Query: 224 ELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVILS 283
           ELEYA  +C+AV EVI P+ +RP+I NLPATVEM TPN+YADSIEW  R+ A  E++ILS
Sbjct: 189 ELEYAVDICNAVAEVIDPSIDRPLILNLPATVEMATPNIYADSIEWFKRHFARPEAMILS 248

Query: 284 LHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQIDFS 343
           +HPHNDRGT VAAAEL   AGADR+EGCLFGNGERTGNVCLVTLG+NLF++GVDP+IDF 
Sbjct: 249 VHPHNDRGTGVAAAELAVQAGADRVEGCLFGNGERTGNVCLVTLGMNLFTQGVDPEIDFG 308

Query: 344 NIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDVDD 403
           +ID IRR VEYCN+LPV ERHPY GDLV+TAFSGSHQDAI KGL A++ +AD A   V+ 
Sbjct: 309 DIDSIRRKVEYCNRLPVPERHPYAGDLVFTAFSGSHQDAIKKGLQALESEADQAGVAVEQ 368

Query: 404 MLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVIQK 463
             W VPYLP+DP+D+GR YEAVIRVNSQSGKGGV+YIM  D+G  LPRR+QIEFSQ IQK
Sbjct: 369 YPWAVPYLPVDPKDIGRNYEAVIRVNSQSGKGGVSYIMHHDYGFDLPRRMQIEFSQAIQK 428

Query: 464 IAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKINGV 523
               T   G EV+P+E+ D F  EY    +P  R+          G   ++ A V ++G 
Sbjct: 429 ---HTDHSGREVTPEEIHDVFRREYHPEYQPNARLAVGSCNTSTHGDEVTVEAVVTLDGQ 485

Query: 524 ETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIASPAQP 583
           E +I G GNGPL+AFV ALA+V   V V +Y +H++S G DA++AAYVE ++        
Sbjct: 486 EHKIIGDGNGPLSAFVSALAEVDVAVEVQEYVQHSLSTGSDAKSAAYVECAI-------- 537

Query: 584 GEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSAVNR 641
           GE                              +TVWG G+  +IT A+LRA+ SAVNR
Sbjct: 538 GE------------------------------RTVWGAGVHSNITLATLRALASAVNR 565


Lambda     K      H
   0.317    0.133    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: 1653
Number of extensions: 76
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 644
Length of database: 956
Length adjustment: 41
Effective length of query: 603
Effective length of database: 915
Effective search space:   551745
Effective search space used:   551745
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: 55 (25.8 bits)

Align candidate WP_025273525.1 HALAL_RS19070 (2-isopropylmalate synthase)
to HMM TIGR00970 (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/TIGR00970.hmm
# target sequence database:        /tmp/gapView.1812010.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00970  [M=564]
Accession:   TIGR00970
Description: leuA_yeast: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-255  834.1   0.0   3.4e-255  833.8   0.0    1.1  1  NCBI__GCF_000527155.1:WP_025273525.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000527155.1:WP_025273525.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.8   0.0  3.4e-255  3.4e-255       3     562 ..       9     566 ..       7     568 .. 0.97

  Alignments for each domain:
  == domain 1  score: 833.8 bits;  conditional E-value: 3.4e-255
                             TIGR00970   3 kkykpfk...aiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsa 72 
                                            +y+pf+    ++l++r+wpd++i++ap w++vdlrdGnqalidpm+ erkk +f+ lv++G+keievgfp+a
  NCBI__GCF_000527155.1:WP_025273525.1   9 TRYRPFHeeiRVHLPDRTWPDRIIDHAPTWCAVDLRDGNQALIDPMDLERKKTMFQTLVDMGYKEIEVGFPAA 81 
                                           79****9877789************************************************************ PP

                             TIGR00970  73 sqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevla 145
                                           sqtdfdfvr +ie+  ip dv+iqvltq+r++likrt+e+l+Ga++aivh+yn+ts+l+r+vvf+a++  + +
  NCBI__GCF_000527155.1:WP_025273525.1  82 SQTDFDFVRALIEEERIPADVSIQVLTQCRDHLIKRTFESLRGARQAIVHFYNSTSILQRKVVFQADKPSITK 154
                                           ************************************************************************* PP

                             TIGR00970 146 lavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatp 218
                                           +a++g++l  k + d   +++t+ ++eyspesf++tele+av++c+av evi+p+ +rp+i+nlpatve+atp
  NCBI__GCF_000527155.1:WP_025273525.1 155 IATDGAELCLKYAAD--ITPDTDIRYEYSPESFTGTELEYAVDICNAVAEVIDPSIDRPLILNLPATVEMATP 225
                                           *****7776666544..4689**************************************************** PP

                             TIGR00970 219 nvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlyt 291
                                           n+yadsie++ +++a  e +ils+hphndrGt+vaaael + aGadr+eGclfGnGertGnv+lvtl++nl+t
  NCBI__GCF_000527155.1:WP_025273525.1 226 NIYADSIEWFKRHFARPEAMILSVHPHNDRGTGVAAAELAVQAGADRVEGCLFGNGERTGNVCLVTLGMNLFT 298
                                           ************************************************************************* PP

                             TIGR00970 292 qGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaa.....dtlw 359
                                           qGv+p++df d+d+i+r ve+cn++pv erhpy+Gdlv+tafsGshqdaikkGl+al+ ++++a     +  w
  NCBI__GCF_000527155.1:WP_025273525.1 299 QGVDPEIDFGDIDSIRRKVEYCNRLPVPERHPYAGDLVFTAFSGSHQDAIKKGLQALESEADQAgvaveQYPW 371
                                           **************************************************************9989997888* PP

                             TIGR00970 360 kvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisd 432
                                            vpylp+dpkd+gr+yeavirvnsqsGkGGv+y+++ d+G+dlprr+qiefs+++++++d  G+e++++ei d
  NCBI__GCF_000527155.1:WP_025273525.1 372 AVPYLPVDPKDIGRNYEAVIRVNSQSGKGGVSYIMHHDYGFDLPRRMQIEFSQAIQKHTDHSGREVTPEEIHD 444
                                           ************************************************************************* PP

                             TIGR00970 433 lfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladllnvdvavad 505
                                           +f+ ey+ + ++  r+ + + + + +G ++ +++avv ++g++ +i G GnGplsa+v ala++  v v+v +
  NCBI__GCF_000527155.1:WP_025273525.1 445 VFRREYHPEYQPNARLAVGSCNTSTHG-DEVTVEAVVTLDGQEHKIIGDGNGPLSAFVSALAEVD-VAVEVQE 515
                                           ***************************.77889******************************98.******* PP

                             TIGR00970 506 ysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavnra 562
                                           y +h+l++G+dak+a+yve ++ + +      vwG G+++++t a+lra+ savnr+
  NCBI__GCF_000527155.1:WP_025273525.1 516 YVQHSLSTGSDAKSAAYVECAIGERT------VWGAGVHSNITLATLRALASAVNRV 566
                                           *******************9988776......9**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (956 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 47.07
//
[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