Alignments for a candidate for leuA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Magnetospirillum magneticum AMB-1

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_011385828.1 AMB_RS17550 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>NCBI__GCF_000009985.1:WP_011385828.1
          Length = 553

 Score =  592 bits (1526), Expect = e-173
 Identities = 318/589 (53%), Positives = 397/589 (67%), Gaps = 51/589 (8%)

Query: 56  IRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDLLVRMGYKEIEVGFP 115
           IRL  R WPD  I R P+WC+VDLRDGNQALIDPM   RK  ++  L+ MG+KEIEVGFP
Sbjct: 15  IRLAQRRWPDATITRPPVWCSVDLRDGNQALIDPMGSERKMALWQTLIGMGFKEIEVGFP 74

Query: 116 SASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGAPRAIVHFYNSTSIL 175
           +ASQTDFDFVR +IE G IP+DVTIQVL Q R ELI RTF+A +GA R IVH YNSTS  
Sbjct: 75  AASQTDFDFVRLLIEGGHIPEDVTIQVLVQSRDELIRRTFEALAGARRVIVHMYNSTSEA 134

Query: 176 QRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYTGTELEYAKQVCDAV 235
           QRR+VF  +R     +A  G R   E +A  P  +  F+YSPES+TGTE ++A  + + V
Sbjct: 135 QRRIVFGIDRQGCIDLALSGVRLVRELSAARPEGEVVFQYSPESFTGTEPDFAMDIVEKV 194

Query: 236 GEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVILSLHPHNDRGTAVA 295
            E    TPER +I NLPATVEM+TPN+YAD IEW   ++ NR+S+I+S+HPHNDRGT VA
Sbjct: 195 AEAWGATPERKMICNLPATVEMSTPNIYADVIEWFCAHVKNRDSLIVSVHPHNDRGTGVA 254

Query: 296 AAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQIDFSNIDEIRRTVEYC 355
           AAEL   AGADR+EG LFGNGERTGNV +VTL LNL+++GVDP +D S+ID +RRT E C
Sbjct: 255 AAELAVMAGADRVEGTLFGNGERTGNVDVVTLALNLYTQGVDPALDLSDIDTVRRTAEQC 314

Query: 356 NQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDVDDMLWQVPYLPIDP 415
             LPVH RHPY G+LVYTAFSGSHQDAI KG  A K          +D +W+VPYLPIDP
Sbjct: 315 TGLPVHPRHPYAGELVYTAFSGSHQDAIKKGFSARK--------KANDPVWEVPYLPIDP 366

Query: 416 RDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVIQKIAEGTAGEGGEV 475
            DVGR+YEAVIR+NSQSGKGG+A +++ DHGL +PR LQI+F++V+Q +A+     G E+
Sbjct: 367 ADVGRSYEAVIRINSQSGKGGIAAVLERDHGLEIPRPLQIDFARVVQAMADKV---GREL 423

Query: 476 SPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKINGVETEISGSGNGPL 535
              E+  AF++ YL    PLE +  +   ++  G T  ++AT++  GVE  I G GNGPL
Sbjct: 424 DSGEIMAAFSQTYLKD-WPLELV-DYETHSEGRGATRMLSATIRDKGVEKRIEGRGNGPL 481

Query: 536 AAFVHAL-ADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIASPAQPGEAGRHASDPV 594
            AF+HAL   +G  V V DY+EHA+ +G +AQAA YVE +         GE G       
Sbjct: 482 DAFIHALETGLGRKVKVRDYHEHALGSGSEAQAACYVEIA---------GEGG------- 525

Query: 595 TIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSAVNRAA 643
                                 +V G  +  SIT ASL+AVVSA+NRAA
Sbjct: 526 ---------------------GSVHGAALDSSITMASLKAVVSALNRAA 553


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: 908
Number of extensions: 38
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: 644
Length of database: 553
Length adjustment: 37
Effective length of query: 607
Effective length of database: 516
Effective search space:   313212
Effective search space used:   313212
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: 53 (25.0 bits)

Align candidate WP_011385828.1 AMB_RS17550 (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.565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-237  774.0   0.0   5.1e-237  773.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385828.1  AMB_RS17550 2-isopropylmalate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385828.1  AMB_RS17550 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  773.8   0.0  5.1e-237  5.1e-237       2     563 ..       6     553 .]       5     553 .] 0.96

  Alignments for each domain:
  == domain 1  score: 773.8 bits;  conditional E-value: 5.1e-237
                                 TIGR00970   2 skkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfp 70 
                                               s ky+ + ai+l++r+wpd  itr p w+svdlrdGnqalidpm +erk  +++ l+ +Gfkeievgfp
  lcl|NCBI__GCF_000009985.1:WP_011385828.1   6 STKYRAYPAIRLAQRRWPDATITRPPVWCSVDLRDGNQALIDPMGSERKMALWQTLIGMGFKEIEVGFP 74 
                                               78******************************************************************* PP

                                 TIGR00970  71 sasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfras 139
                                               +asqtdfdfvr +ie g ip+dvtiqvl+qsr+eli+rt+eal+Ga++ ivh+yn+ts+ +r++vf  +
  lcl|NCBI__GCF_000009985.1:WP_011385828.1  75 AASQTDFDFVRLLIEGGHIPEDVTIQVLVQSRDELIRRTFEALAGARRVIVHMYNSTSEAQRRIVFGID 143
                                               ********************************************************************* PP

                                 TIGR00970 140 reevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifn 208
                                               r+ +++la+ g +lvr+l    a ++e +  f+yspesf++te++fa+++ e v e++  t+er +i n
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 144 RQGCIDLALSGVRLVRELS---AARPEGEVVFQYSPESFTGTEPDFAMDIVEKVAEAWGATPERKMICN 209
                                               ***********88888775...667788999************************************** PP

                                 TIGR00970 209 lpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGert 277
                                               lpatve++tpn+yad ie+++ ++ +r+++i+s+hphndrGt+vaaael ++aGadr+eG lfGnGert
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 210 LPATVEMSTPNIYADVIEWFCAHVKNRDSLIVSVHPHNDRGTGVAAAELAVMAGADRVEGTLFGNGERT 278
                                               ********************************************************************* PP

                                 TIGR00970 278 GnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGld 346
                                               Gnvd+vtlalnlytqGv+p ld+sd+d ++r+ e+c  +pvh+rhpy+G+lv+tafsGshqdaikkG+ 
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 279 GNVDVVTLALNLYTQGVDPALDLSDIDTVRRTAEQCTGLPVHPRHPYAGELVYTAFSGSHQDAIKKGFS 347
                                               ********************************************************************9 PP

                                 TIGR00970 347 aldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvk 415
                                               a +k   a+d++w+vpylp+dp dvgr yeavir+nsqsGkGG+a vl +d+Gl++pr lqi+f++vv+
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 348 ARKK---ANDPVWEVPYLPIDPADVGRSYEAVIRINSQSGKGGIAAVLERDHGLEIPRPLQIDFARVVQ 413
                                               9765...3488********************************************************** PP

                                 TIGR00970 416 diadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGt.eskvitavvkikgekkdieGsGn 483
                                                +ad  G+el+s+ei+ +f ++yl  + +   ++lvdy+ +++G   ++++ a+++ kg++k ieG Gn
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 414 AMADKVGRELDSGEIMAAFSQTYLK-DWP---LELVDYETHSEGRgATRMLSATIRDKGVEKRIEGRGN 478
                                               ***********************98.444...4566777777765157899****************** PP

                                 TIGR00970 484 GplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsasl 552
                                               Gpl a+++al+  l  +v+v dy ehalgsG++a+aa+yve++ +       + v G  +++++t asl
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 479 GPLDAFIHALETGLGRKVKVRDYHEHALGSGSEAQAACYVEIAGEG-----GGSVHGAALDSSITMASL 542
                                               *****************************************97654.....4689************** PP

                                 TIGR00970 553 ravlsavnraa 563
                                               +av+sa+nraa
  lcl|NCBI__GCF_000009985.1:WP_011385828.1 543 KAVVSALNRAA 553
                                               ********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (553 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 7.82
//
[ok]

This GapMind analysis is from Apr 09 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