Alignments for a candidate for leuA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Marinobacter adhaerens HP15

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate GFF555 HP15_538 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Marino:GFF555
          Length = 516

 Score =  649 bits (1675), Expect = 0.0
 Identities = 321/500 (64%), Positives = 399/500 (79%)

Query: 1   MTQTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAV 60
           M  T+ ++IFDTTLRDGEQSPGA M K EK+R+A+ LEKL VD+IEAGFA AS GDFEAV
Sbjct: 1   MPATDHLVIFDTTLRDGEQSPGATMNKAEKLRIAKALEKLRVDVIEAGFAIASQGDFEAV 60

Query: 61  NAIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQV 120
            AIA++I  ST+CSL+RA+++DI +A EA+ PA + RIHTFIATSPIHM++KL+M+P +V
Sbjct: 61  KAIAESIKDSTICSLARALDKDIDRAAEAIRPAQRGRIHTFIATSPIHMKHKLQMQPDEV 120

Query: 121 IEAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPY 180
           IE AV++VK AR + DDVEFSCEDA RSE+DFL  I  A I+AGA+TINIPDTVGY+IP 
Sbjct: 121 IEQAVRSVKRARSHVDDVEFSCEDAGRSELDFLCRIIEAAIDAGASTINIPDTVGYAIPE 180

Query: 181 KTEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGN 240
           +  E  R+L+ + PN  K ++S HCHNDLGLAV+NSLAA+  GARQVECT+NGLGERAGN
Sbjct: 181 QFGETIRQLLNRIPNADKAIFSVHCHNDLGLAVSNSLAAVSQGARQVECTINGLGERAGN 240

Query: 241 ASVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESG 300
           A++EEIVMA++ R DLF ++T ID   IVP+S+LVSTITG+PVQPNKAIVGANAF+HESG
Sbjct: 241 AALEEIVMAVRTRQDLFHIDTRIDAQHIVPASRLVSTITGFPVQPNKAIVGANAFAHESG 300

Query: 301 IHQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAF 360
           IHQDGVLKHRETYEIM A+ VGW TN L LGK SGRNAF+T+L +LGI+ E+E  LN AF
Sbjct: 301 IHQDGVLKHRETYEIMRAQDVGWHTNSLVLGKHSGRNAFRTRLLELGIQFETETELNEAF 360

Query: 361 ARFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGE 420
            RFK LAD K EIFDEDL A+ SD         Y  +  ++ +ETG  P+A++  S+ G+
Sbjct: 361 TRFKALADLKHEIFDEDLQAIASDTRQKEEDGRYGLVCMQVCSETGVVPKANLTLSVDGK 420

Query: 421 EKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNG 480
           E +  A GSGPVDA FKAIES+  SG  LQ+YSVN +T GT++QGE +VRL RG R+VNG
Sbjct: 421 EHKVEAEGSGPVDATFKAIESLVDSGCNLQLYSVNNITSGTDAQGEVTVRLERGGRIVNG 480

Query: 481 QGADTDVLVATAKAYLSALS 500
            GADTD+++A+AKAY+ AL+
Sbjct: 481 VGADTDIIIASAKAYIEALN 500


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: 677
Number of extensions: 25
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: 517
Length of database: 516
Length adjustment: 35
Effective length of query: 482
Effective length of database: 481
Effective search space:   231842
Effective search space used:   231842
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 GFF555 HP15_538 (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.17172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     2e-226  738.1   6.7   2.2e-226  738.0   6.7    1.0  1  lcl|FitnessBrowser__Marino:GFF555  HP15_538 2-isopropylmalate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF555  HP15_538 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  738.0   6.7  2.2e-226  2.2e-226       2     494 .]       7     500 ..       6     500 .. 0.99

  Alignments for each domain:
  == domain 1  score: 738.0 bits;  conditional E-value: 2.2e-226
                          TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekd 77 
                                        ++ifdttlrdGeq+pga+++  ekl+iakale+l vd+ieaGf+++s+gdfeav+ ia+++k++++++lara++kd
  lcl|FitnessBrowser__Marino:GFF555   7 LVIFDTTLRDGEQSPGATMNKAEKLRIAKALEKLRVDVIEAGFAIASQGDFEAVKAIAESIKDSTICSLARALDKD 82 
                                        68************************************************************************** PP

                          TIGR00973  78 idaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvve 153
                                        id aaea++pa++ rihtfiats+ih+++kl+++ dev+e++v+ vk+a+++vddvefs+edagr+el+fl+r++e
  lcl|FitnessBrowser__Marino:GFF555  83 IDRAAEAIRPAQRGRIHTFIATSPIHMKHKLQMQPDEVIEQAVRSVKRARSHVDDVEFSCEDAGRSELDFLCRIIE 158
                                        **************************************************************************** PP

                          TIGR00973 154 aaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGi 229
                                        aai+aGa+tiniPdtvGya+P+++ge i++l +++Pn dkai+svhch+dlGlav+nslaav +GarqvectinG+
  lcl|FitnessBrowser__Marino:GFF555 159 AAIDAGASTINIPDTVGYAIPEQFGETIRQLLNRIPNADKAIFSVHCHNDLGLAVSNSLAAVSQGARQVECTINGL 234
                                        **************************************************************************** PP

                          TIGR00973 230 GeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknk 305
                                        GeraGnaalee+vma+++r+d+++++t i+ ++i  +srlvs +tg +vq+nkaivG+nafahesGihqdGvlk++
  lcl|FitnessBrowser__Marino:GFF555 235 GERAGNAALEEIVMAVRTRQDLFHIDTRIDAQHIVPASRLVSTITGFPVQPNKAIVGANAFAHESGIHQDGVLKHR 310
                                        **************************************************************************** PP

                          TIGR00973 306 etyeilspesiGlkkeklvlgkrsGraalkkrleelGfkld.eeeldklfekfkeladkkkevfdedlealvleel 380
                                        etyei++++++G +++ lvlgk+sGr+a+++rl elG++++ e+el+++f++fk lad k+e+fdedl+a++++  
  lcl|FitnessBrowser__Marino:GFF555 311 ETYEIMRAQDVGWHTNSLVLGKHSGRNAFRTRLLELGIQFEtETELNEAFTRFKALADLKHEIFDEDLQAIASDTR 386
                                        ***************************************863789******************************* PP

                          TIGR00973 381 rqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkd 456
                                        ++ee+ ++ l+ +qv s +  vp a ++l v+g+e++  a G+Gpvda++kaie +++   +l+ ys++  ++g+d
  lcl|FitnessBrowser__Marino:GFF555 387 QKEEDGRYGLVCMQVCSETGVVPKANLTLSVDGKEHKVEAEGSGPVDATFKAIESLVDSGCNLQLYSVNNITSGTD 462
                                        **************************************************************************** PP

                          TIGR00973 457 algevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                        a+gev+v+le  g+ ++G+g++tdi+ asakay++aln
  lcl|FitnessBrowser__Marino:GFF555 463 AQGEVTVRLERGGRIVNGVGADTDIIIASAKAYIEALN 500
                                        *************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (516 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: 12.21
//
[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