Alignments for a candidate for leuA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Phaeobacter inhibens BS107

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate GFF2606 PGA1_c26470 2-isopropylmalate synthase LeuA

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Phaeo:GFF2606
          Length = 523

 Score =  484 bits (1246), Expect = e-141
 Identities = 252/498 (50%), Positives = 341/498 (68%), Gaps = 4/498 (0%)

Query: 5   NRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIA 64
           +RV+IFDTTLRDGEQSPGA MT +EK+ +A  L+ +GVDIIEAGF  AS GDF+AV+ IA
Sbjct: 8   DRVLIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFKAVSEIA 67

Query: 65  KTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAA 124
           +    S +C L+RA  +DI +  EAV  A + RIHTFI TSP+H      +   ++ E  
Sbjct: 68  ERSKNSRICGLARANFKDIDRCAEAVKRAAQPRIHTFIGTSPLHRAIP-NLTKDEMAEKI 126

Query: 125 VKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEE 184
              V  AR   D+V++S  DA R+E D+L  +    I+AGATTINIPDTVGY+ P ++ +
Sbjct: 127 HDTVTHARNLVDNVQWSPMDATRTEWDYLCRVIEIAIKAGATTINIPDTVGYTAPVESAD 186

Query: 185 FFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVE 244
             + LI   P    V+++ HCHNDLG+A ANSLAA+ GGARQ+ECT+NGLGERAGN ++E
Sbjct: 187 LIKRLIETVPGADDVIFATHCHNDLGMATANSLAAVAGGARQIECTINGLGERAGNTALE 246

Query: 245 EIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304
           E+VMALKVR+D+    TGIDT +I+  S+ VST++G+ VQPNKAIVG NAF+HESGIHQD
Sbjct: 247 EVVMALKVRNDIMPFTTGIDTQKIMHISRRVSTVSGFVVQPNKAIVGKNAFAHESGIHQD 306

Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364
           G+LK++ET+EIM  E VG A   L LGK SGR A + KL+ LG E+  +  L   F RFK
Sbjct: 307 GMLKNKETFEIMRPEDVGIAGTSLPLGKHSGRAALRDKLSQLGFEV-GDNQLKDLFVRFK 365

Query: 365 ELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKRA 424
           ELAD+K+E+FD+D+ AL+         +  K +S K+   TG    A +   ++G++   
Sbjct: 366 ELADRKKEVFDDDIIALM--RTSGDEDDHLKLVSMKVVCGTGGPAEATLEMEVEGKDVSE 423

Query: 425 SATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGAD 484
           +A G GPVDA F+AI  +  + A LQ+Y V+AVT+GT++Q   SVRL     +  G+ A+
Sbjct: 424 TAEGDGPVDAAFRAIRKIHPNSAHLQLYQVHAVTEGTDAQATVSVRLEENGVIATGESAN 483

Query: 485 TDVLVATAKAYLSALSKL 502
           TD +VA+A AY+ AL++L
Sbjct: 484 TDTVVASAAAYIGALNRL 501


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: 636
Number of extensions: 21
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: 523
Length adjustment: 35
Effective length of query: 482
Effective length of database: 488
Effective search space:   235216
Effective search space used:   235216
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 GFF2606 PGA1_c26470 (2-isopropylmalate synthase LeuA)
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.18265.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.6e-206  671.8   4.1     3e-206  671.6   4.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2606  PGA1_c26470 2-isopropylmalate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2606  PGA1_c26470 2-isopropylmalate synthase LeuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.6   4.1    3e-206    3e-206       1     494 []       9     499 ..       9     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.6 bits;  conditional E-value: 3e-206
                          TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravek 76 
                                        rvlifdttlrdGeq+pga++t +ekl+ia+ l+++gvdiieaGfp++s+gdf+av +ia++ kn+r++glara  k
  lcl|FitnessBrowser__Phaeo:GFF2606   9 RVLIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFKAVSEIAERSKNSRICGLARANFK 84 
                                        799************************************************************************* PP

                          TIGR00973  77 didaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvv 152
                                        did  aea+k a++ rihtfi ts++h++     tkde+ e+i+ +v++a+n+vd+v++s+ da+rte ++l+rv+
  lcl|FitnessBrowser__Phaeo:GFF2606  85 DIDRCAEAVKRAAQPRIHTFIGTSPLHRAIP-NLTKDEMAEKIHDTVTHARNLVDNVQWSPMDATRTEWDYLCRVI 159
                                        ***************************9875.789***************************************** PP

                          TIGR00973 153 eaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinG 228
                                        e ai+aGattiniPdtvGy++P e ++lik+l e+vP+ d++i++ hch+dlG+a+anslaav  Garq+ectinG
  lcl|FitnessBrowser__Phaeo:GFF2606 160 EIAIKAGATTINIPDTVGYTAPVESADLIKRLIETVPGADDVIFATHCHNDLGMATANSLAAVAGGARQIECTING 235
                                        **************************************************************************** PP

                          TIGR00973 229 iGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlkn 304
                                        +GeraGn+aleevvmalkvr+d+++ +tgi+t++i+++sr vs ++g +vq+nkaivG+nafahesGihqdG+lkn
  lcl|FitnessBrowser__Phaeo:GFF2606 236 LGERAGNTALEEVVMALKVRNDIMPFTTGIDTQKIMHISRRVSTVSGFVVQPNKAIVGKNAFAHESGIHQDGMLKN 311
                                        **************************************************************************** PP

                          TIGR00973 305 ketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleel 380
                                        ket+ei++pe++G+  + l lgk+sGraal+++l++lGf++ +++l+ lf +fkelad+kkevfd+d+ al+ ++ 
  lcl|FitnessBrowser__Phaeo:GFF2606 312 KETFEIMRPEDVGIAGTSLPLGKHSGRAALRDKLSQLGFEVGDNQLKDLFVRFKELADRKKEVFDDDIIALMRTSG 387
                                        **********************************************************************998765 PP

                          TIGR00973 381 rqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkd 456
                                           e+++lkl++++v +g+   + at++++v+g++ +++a G Gpvda ++ai ki   + +l+ y+++a++eg+d
  lcl|FitnessBrowser__Phaeo:GFF2606 388 D--EDDHLKLVSMKVVCGTGGPAEATLEMEVEGKDVSETAEGDGPVDAAFRAIRKIHPNSAHLQLYQVHAVTEGTD 461
                                        5..66778******************************************************************** PP

                          TIGR00973 457 algevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                        a++ v+v+le ng+ ++G +++td v asa ay+ aln
  lcl|FitnessBrowser__Phaeo:GFF2606 462 AQATVSVRLEENGVIATGESANTDTVVASAAAYIGALN 499
                                        ************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (523 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: 12.57
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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 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