Alignments for a candidate for leuA in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Sinorhizobium fredii NGR234

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate WP_012708863.1 NGR_RS22895 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>NCBI__GCF_000018545.1:WP_012708863.1
          Length = 569

 Score =  620 bits (1599), Expect = 0.0
 Identities = 313/579 (54%), Positives = 410/579 (70%), Gaps = 24/579 (4%)

Query: 35  SMPVNRYMPFEVEVE-----DISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPER 89
           S P+   MP E  V+      ++LPDRTWP K I  AP WC+VDLRDGNQ+L+DPM  +R
Sbjct: 5   SHPIKTGMP-EAAVKYQAYPQVALPDRTWPSKSIDKAPIWCSVDLRDGNQSLVDPMGHDR 63

Query: 90  KRRMFELLVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRT 149
           K RMF LLV MGFKEIE+GFPSASQTDFDF R  +E+G +P DV++QVLVQ R  LI RT
Sbjct: 64  KARMFHLLVDMGFKEIEIGFPSASQTDFDFARWCVEEGDVPADVSLQVLVQCRPELITRT 123

Query: 150 FEACEGAKNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQ 209
           FEA +GA   IVHFYNSTS LQR VVF  D   +K++ATDAA++I  +A       +R++
Sbjct: 124 FEALDGAHKPIVHFYNSTSELQRRVVFAKDVAGIKQIATDAAKMITDMAAK-AGGGYRFE 182

Query: 210 YSPESFTGTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNL 269
           YSPESFTGTE+E A E+ +AV E++ PTP+N +IINLPSTVEM TPN+YAD IEWM RNL
Sbjct: 183 YSPESFTGTELEVALEICNAVTEIVRPTPDNKLIINLPSTVEMATPNIYADQIEWMCRNL 242

Query: 270 NRRDSIILSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQ 329
           + R+++++SLHPHNDRGTG+ A ELG MAGADR+EG LFGNGERTGNV +VTLALNM TQ
Sbjct: 243 DNRENLLISLHPHNDRGTGIAATELGLMAGADRVEGTLFGNGERTGNVDVVTLALNMFTQ 302

Query: 330 GVDPQLDFTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKV 389
           GVDP+LD +DI +I+   EY NQ+ +PERHPY G+LV+TAFSGSHQDA+NKG+ A+    
Sbjct: 303 GVDPKLDCSDIERIKEVYEYSNQMVIPERHPYVGELVYTAFSGSHQDAINKGMKAL---- 358

Query: 390 QPGASSTEVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGL 449
                      +Q     WEVPYLPIDP+DVGR YEA+IR+NSQSGKGG+AYIM+ D+G+
Sbjct: 359 -----------KQANKPTWEVPYLPIDPRDVGRSYEAIIRINSQSGKGGIAYIMQEDYGI 407

Query: 450 QIPRSMQVEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERT-APVEQIALRVENAQTEN 508
            +PR++Q+EF   +Q +TD EG E+ SK +   F   Y+E+  A ++ +           
Sbjct: 408 NLPRNLQIEFREDIQRITDEEGKELPSKRIHQRFVERYVEQPGARIKFVDHHTYPVSDHK 467

Query: 509 EDASITAELIHNGKDVTVDGRGNGPLAAYANALE-KLGIDVEIQEYNQHARTSGDDAEAA 567
               + AE+   G+   ++G+G GP+  + NAL   LG+++ + +Y++H+   G +A A 
Sbjct: 468 SLRVVAAEITDRGETKRIEGKGTGPIDGFINALSIYLGVELSVADYSEHSLQHGSNAAAI 527

Query: 568 AYVLAEVNGRKVWGVGIAGSITYASLKAVTSAVNRALDV 606
           AYV  E  G  ++G GI  +I  ASL+A+ SA NR L++
Sbjct: 528 AYVEVEHPGGTLFGAGINTNIVAASLEAIVSAANRVLEL 566


Lambda     K      H
   0.316    0.133    0.390 

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: 980
Number of extensions: 38
Number of successful extensions: 5
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: 616
Length of database: 569
Length adjustment: 37
Effective length of query: 579
Effective length of database: 532
Effective search space:   308028
Effective search space used:   308028
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_012708863.1 NGR_RS22895 (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.3062307.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-232  758.5   0.0   2.7e-232  758.2   0.0    1.0  1  NCBI__GCF_000018545.1:WP_012708863.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012708863.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  758.2   0.0  2.7e-232  2.7e-232       3     562 ..      17     563 ..      15     565 .. 0.96

  Alignments for each domain:
  == domain 1  score: 758.2 bits;  conditional E-value: 2.7e-232
                             TIGR00970   3 kkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsasqt 75 
                                            ky+ +  + l++r+wp k i++ap w+svdlrdGnq+l+dpm  +rk r+f+llv++Gfkeie+gfpsasqt
  NCBI__GCF_000018545.1:WP_012708863.1  17 VKYQAYPQVALPDRTWPSKSIDKAPIWCSVDLRDGNQSLVDPMGHDRKARMFHLLVDMGFKEIEIGFPSASQT 89 
                                           59*********************************************************************** PP

                             TIGR00970  76 dfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlalav 148
                                           dfdf r  +e+g +p dv++qvl+q+r+eli rt+eal Ga+k ivh+yn+ts+l+r+vvf ++ + + ++a+
  NCBI__GCF_000018545.1:WP_012708863.1  90 DFDFARWCVEEGDVPADVSLQVLVQCRPELITRTFEALDGAHKPIVHFYNSTSELQRRVVFAKDVAGIKQIAT 162
                                           ************************************************************************* PP

                             TIGR00970 149 egsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnvy 221
                                           +++k+++      a + +  ++feyspesf++tele a+e+c+av e+++pt+++ +i nlp+tve+atpn+y
  NCBI__GCF_000018545.1:WP_012708863.1 163 DAAKMITD----MAAKAGGGYRFEYSPESFTGTELEVALEICNAVTEIVRPTPDNKLIINLPSTVEMATPNIY 231
                                           **766654....45566889***************************************************** PP

                             TIGR00970 222 adsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGv 294
                                           ad+ie++++n+ +re++++slhphndrGt++aa+elGl+aGadr+eG lfGnGertGnvd+vtlaln++tqGv
  NCBI__GCF_000018545.1:WP_012708863.1 232 ADQIEWMCRNLDNRENLLISLHPHNDRGTGIAATELGLMAGADRVEGTLFGNGERTGNVDVVTLALNMFTQGV 304
                                           ************************************************************************* PP

                             TIGR00970 295 spnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpld 367
                                           +p+ld sd++ i++v e+ n++ + erhpy G+lv+tafsGshqdai+kG++al++ +   ++ w+vpylp+d
  NCBI__GCF_000018545.1:WP_012708863.1 305 DPKLDCSDIERIKEVYEYSNQMVIPERHPYVGELVYTAFSGSHQDAINKGMKALKQAN---KPTWEVPYLPID 374
                                           ****************************************************987644...579********* PP

                             TIGR00970 368 pkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyll 440
                                           p+dvgr yea+ir+nsqsGkGG+ay+++ d+G++lpr+lqief + ++ i+d +Gkel sk i + f e y  
  NCBI__GCF_000018545.1:WP_012708863.1 375 PRDVGRSYEAIIRINSQSGKGGIAYIMQEDYGINLPRNLQIEFREDIQRITDEEGKELPSKRIHQRFVERYVE 447
                                           ***********************************************************************87 PP

                             TIGR00970 441 .nveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladllnvdvavadysehalg 512
                                            +   ++ +  ++y v+d+    +v+ a +  +ge+k ieG G Gp+  +++al+  l v+++vadyseh+l 
  NCBI__GCF_000018545.1:WP_012708863.1 448 qPGARIKFVDHHTYPVSDHK-SLRVVAAEITDRGETKRIEGKGTGPIDGFINALSIYLGVELSVADYSEHSLQ 519
                                           14455666677888898887.899************************************************* PP

                             TIGR00970 513 sGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavnra 562
                                            G++a a +yve+          +t +G Gi++++ +asl a++sa nr+
  NCBI__GCF_000018545.1:WP_012708863.1 520 HGSNAAAIAYVEVEHP------GGTLFGAGINTNIVAASLEAIVSAANRV 563
                                           ************8654......467***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (569 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 26.91
//
[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 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