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_043745065.1 AMB_RS17765 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000009985.1:WP_043745065.1
          Length = 514

 Score =  560 bits (1443), Expect = e-164
 Identities = 294/512 (57%), Positives = 373/512 (72%), Gaps = 3/512 (0%)

Query: 5   NRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIA 64
           NRVIIFDTTLRDGEQSPGA+M  EEK+R+A  LE++GVD+IEAGF  AS GDFEAV A+A
Sbjct: 4   NRVIIFDTTLRDGEQSPGASMNLEEKVRIALVLEEMGVDVIEAGFPIASNGDFEAVEAVA 63

Query: 65  KTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAA 124
           K +  S +C L+RA + DI +  EA+ PA + RIHTF++TSP+HM+YKL+M+P++V+E  
Sbjct: 64  KAVKTSVICGLARATKGDIERCAEAIRPAARGRIHTFLSTSPLHMKYKLQMEPEKVLEKV 123

Query: 125 VKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEE 184
            ++V  AR+ TDDVE+S ED  R+E DFL     A I AGA TINIPDTVGY++P +   
Sbjct: 124 AESVAYARKLTDDVEWSAEDGSRTEHDFLCRCVEAAIAAGARTINIPDTVGYAVPDEYAA 183

Query: 185 FFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVE 244
               LI + PN  K V S HCHNDLGLAVANSLAA+  GARQ+ECTVNGLGERAGNA++E
Sbjct: 184 LIAMLINRVPNIDKAVLSVHCHNDLGLAVANSLAAVGKGARQIECTVNGLGERAGNAAME 243

Query: 245 EIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304
           EIVMAL+ R DL   +TGI T  I  +S+LVSTITG+ VQPNKAIVG NAF+HESGIHQD
Sbjct: 244 EIVMALRTRPDLLPFKTGIKTENITRASRLVSTITGFVVQPNKAIVGKNAFAHESGIHQD 303

Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364
           GVLKH +TYEIM+ ESVG   + L +GK SGR AFK KL +LG EL  + A+  AF RFK
Sbjct: 304 GVLKHAQTYEIMTPESVGLHRSNLVMGKHSGRAAFKAKLKELGYEL-GDNAIEDAFTRFK 362

Query: 365 ELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEE-PRADIVFSIKGEEKR 423
           +LAD+K+++FDED+ ALV D +   N +  K +S ++   T  + P A +  S+ GE K 
Sbjct: 363 DLADRKKDVFDEDIVALVDDAVVRGN-DRVKLVSLEVLCGTKHQPPSATLELSVDGEVKG 421

Query: 424 ASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGA 483
             ATG GPVDA F AI+++    A LQ+Y V+AVTQGT++Q E +VRL    + VNGQGA
Sbjct: 422 VRATGDGPVDATFNAIKALFPHEARLQLYQVSAVTQGTDAQAEVTVRLEEDGKTVNGQGA 481

Query: 484 DTDVLVATAKAYLSALSKLEFSAAKPKAQGSG 515
           +TD LVA+A+AY++AL+KL     K     +G
Sbjct: 482 ETDTLVASARAYVNALNKLLVKRQKTAPDAAG 513


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: 643
Number of extensions: 23
Number of successful extensions: 3
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: 514
Length adjustment: 35
Effective length of query: 482
Effective length of database: 479
Effective search space:   230878
Effective search space used:   230878
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_043745065.1 AMB_RS17765 (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.11784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.6e-226  736.0   4.2   9.7e-226  735.9   4.2    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043745065.1  AMB_RS17765 2-isopropylmalate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043745065.1  AMB_RS17765 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  735.9   4.2  9.7e-226  9.7e-226       1     494 []       5     498 ..       5     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 735.9 bits;  conditional E-value: 9.7e-226
                                 TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvg 69 
                                               rv+ifdttlrdGeq+pgas+++eek++ia+ le++gvd+ieaGfp++s+gdfeav+ +a++vk+++++g
  lcl|NCBI__GCF_000009985.1:WP_043745065.1   5 RVIIFDTTLRDGEQSPGASMNLEEKVRIALVLEEMGVDVIEAGFPIASNGDFEAVEAVAKAVKTSVICG 73 
                                               79******************************************************************* PP

                                 TIGR00973  70 laravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsae 138
                                               lara++ di+  aea++pa++ rihtf++ts++h+++kl+++ ++vle++ + v+ya++++ddve+sae
  lcl|NCBI__GCF_000009985.1:WP_043745065.1  74 LARATKGDIERCAEAIRPAARGRIHTFLSTSPLHMKYKLQMEPEKVLEKVAESVAYARKLTDDVEWSAE 142
                                               ********************************************************************* PP

                                 TIGR00973 139 dagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGla 207
                                               d +rte +fl+r veaai aGa tiniPdtvGya+P+ey++li+ l ++vPnidka+lsvhch+dlGla
  lcl|NCBI__GCF_000009985.1:WP_043745065.1 143 DGSRTEHDFLCRCVEAAIAAGARTINIPDTVGYAVPDEYAALIAMLINRVPNIDKAVLSVHCHNDLGLA 211
                                               ********************************************************************* PP

                                 TIGR00973 208 vanslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgm 276
                                               vanslaav +Garq+ect+nG+GeraGnaa+ee+vmal++r d+l+ +tgi+t++i r+srlvs +tg 
  lcl|NCBI__GCF_000009985.1:WP_043745065.1 212 VANSLAAVGKGARQIECTVNGLGERAGNAAMEEIVMALRTRPDLLPFKTGIKTENITRASRLVSTITGF 280
                                               ********************************************************************* PP

                                 TIGR00973 277 lvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkl 345
                                               +vq+nkaivG+nafahesGihqdGvlk+ +tyei++pes+Gl++++lv+gk+sGraa+k +l+elG++l
  lcl|NCBI__GCF_000009985.1:WP_043745065.1 281 VVQPNKAIVGKNAFAHESGIHQDGVLKHAQTYEIMTPESVGLHRSNLVMGKHSGRAAFKAKLKELGYEL 349
                                               ********************************************************************* PP

                                 TIGR00973 346 deeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgee.svptatvklkvkg 413
                                                ++ ++ +f++fk+lad+kk+vfded++alv + +++ + +++kl++l+v +g++ + p at++l v+g
  lcl|NCBI__GCF_000009985.1:WP_043745065.1 350 GDNAIEDAFTRFKDLADRKKDVFDEDIVALVDDAVVRGN-DRVKLVSLEVLCGTKhQPPSATLELSVDG 417
                                               ********************************9999765.56**********9752789********** PP

                                 TIGR00973 414 eekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdiv 482
                                               e k   atG Gpvda+++ai+ +   e +l+ y++ a+++g+da++ev+v+le +gk+++G+g++td +
  lcl|NCBI__GCF_000009985.1:WP_043745065.1 418 EVKGVRATGDGPVDATFNAIKALFPHEARLQLYQVSAVTQGTDAQAEVTVRLEEDGKTVNGQGAETDTL 486
                                               ********************************************************************* PP

                                 TIGR00973 483 easakayvnaln 494
                                                asa+ayvnaln
  lcl|NCBI__GCF_000009985.1:WP_043745065.1 487 VASARAYVNALN 498
                                               ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (514 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: 00:00:00.02
# Mc/sec: 11.35
//
[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