Alignments for a candidate for leuA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Sinorhizobium meliloti 1021

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate SMc02717 SMc02717 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__Smeli:SMc02717
          Length = 569

 Score =  625 bits (1612), Expect = 0.0
 Identities = 316/569 (55%), Positives = 409/569 (71%), Gaps = 22/569 (3%)

Query: 40  RYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQ 99
           +Y P+      I LPDRTWP K IT AP WC+VDLRDGNQAL+DPM  +RK RMF LL+ 
Sbjct: 18  KYQPYP----QIVLPDRTWPSKAITEAPIWCSVDLRDGNQALVDPMGHDRKARMFHLLLD 73

Query: 100 MGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNV 159
           MGFKEIE+GFPSASQTD+DF R  +E+G + +DV++QVLVQ R  LI RTFEA EGA   
Sbjct: 74  MGFKEIEIGFPSASQTDYDFARWCVEEGNVSEDVSLQVLVQCRPELIARTFEALEGAHRP 133

Query: 160 IVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTE 219
           IVHFYNSTS LQR VVF  D   +K++ATDAA++I  +A       +R++YSPESFTGTE
Sbjct: 134 IVHFYNSTSELQRRVVFGKDVAGIKQIATDAAKMITDMAAK-AGGGYRFEYSPESFTGTE 192

Query: 220 VEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSL 279
           +E A E+ +AV+E++ PT +N +IINLPSTVEM TPN+YAD IEWM RNL+ R+++I+SL
Sbjct: 193 LEVALEICNAVIEIVRPTADNKLIINLPSTVEMATPNIYADQIEWMCRNLDNRENLIVSL 252

Query: 280 HPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTD 339
           HPHNDRGTG+ A ELG MAGADR+EG LFGNGERTGNV +VTLALNM TQGVDP+LD +D
Sbjct: 253 HPHNDRGTGIAATELGLMAGADRVEGTLFGNGERTGNVDVVTLALNMFTQGVDPKLDCSD 312

Query: 340 IRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVS 399
           I +I+   EY NQ+ +PERHPY G+LV+TAFSGSHQDA+NKG+ A+              
Sbjct: 313 IERIKEVYEYSNQMVIPERHPYVGELVYTAFSGSHQDAINKGMKAI-------------- 358

Query: 400 WEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEF 459
            +Q     WEVPYLPIDP+DVGR YEA+IR+NSQSGKGG+AYI++ D+G+ +PR++Q+EF
Sbjct: 359 -KQANKPTWEVPYLPIDPRDVGRSYEAIIRINSQSGKGGIAYILQEDYGINLPRNLQIEF 417

Query: 460 STVVQNVTDAEGGEVNSKAMWDIFATEYLERT-APVEQIALRVENAQTENEDASITAELI 518
              VQ +TD EG E+ SK +   F   Y+E+  A ++ +      A        + AE+ 
Sbjct: 418 REEVQRITDEEGKELPSKRIHQRFIESYVEQPGARIKFVDHHTYPAGEHKGLRVVAAEIT 477

Query: 519 HNGKDVTVDGRGNGPLAAYANALE-KLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNGR 577
             G+   ++G+G GP+  + NAL   LGI++ + +Y++H+   G +A A AYV  E  G 
Sbjct: 478 DGGETRQIEGKGTGPIDGFINALSIYLGIELSVADYSEHSLQHGSNAAAIAYVEVEYPGG 537

Query: 578 KVWGVGIAGSITYASLKAVTSAVNRALDV 606
           K++GVGI  +I  ASL+A+ SA NR LDV
Sbjct: 538 KLFGVGINTNIVAASLEAIVSAANRVLDV 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: 985
Number of extensions: 35
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 SMc02717 SMc02717 (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.27471.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.5e-232  757.5   0.0   5.3e-232  757.2   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02717  SMc02717 2-isopropylmalate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02717  SMc02717 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  757.2   0.0  5.3e-232  5.3e-232       3     562 ..      17     563 ..      15     565 .. 0.95

  Alignments for each domain:
  == domain 1  score: 757.2 bits;  conditional E-value: 5.3e-232
                           TIGR00970   3 kkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsasqtdf 77 
                                          ky+p+  i l++r+wp k it ap w+svdlrdGnqal+dpm  +rk r+f+ll+++Gfkeie+gfpsasqtd+
  lcl|FitnessBrowser__Smeli:SMc02717  17 VKYQPYPQIVLPDRTWPSKAITEAPIWCSVDLRDGNQALVDPMGHDRKARMFHLLLDMGFKEIEIGFPSASQTDY 91 
                                         59************************************************************************* PP

                           TIGR00970  78 dfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlalavegsk 152
                                         df r  +e+g + +dv++qvl+q+r+eli rt+eal+Ga++ ivh+yn+ts+l+r+vvf ++ + + ++a++++k
  lcl|FitnessBrowser__Smeli:SMc02717  92 DFARWCVEEGNVSEDVSLQVLVQCRPELIARTFEALEGAHRPIVHFYNSTSELQRRVVFGKDVAGIKQIATDAAK 166
                                         *************************************************************************76 PP

                           TIGR00970 153 lvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnvyadsiey 227
                                         +++      a + +  ++feyspesf++tele a+e+c+av e+++pt+++ +i nlp+tve+atpn+yad+ie+
  lcl|FitnessBrowser__Smeli:SMc02717 167 MITD----MAAKAGGGYRFEYSPESFTGTELEVALEICNAVIEIVRPTADNKLIINLPSTVEMATPNIYADQIEW 237
                                         6654....45566889*********************************************************** PP

                           TIGR00970 228 lstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldfsd 302
                                         +++n+ +re++i+slhphndrGt++aa+elGl+aGadr+eG lfGnGertGnvd+vtlaln++tqGv+p+ld sd
  lcl|FitnessBrowser__Smeli:SMc02717 238 MCRNLDNRENLIVSLHPHNDRGTGIAATELGLMAGADRVEGTLFGNGERTGNVDVVTLALNMFTQGVDPKLDCSD 312
                                         *************************************************************************** PP

                           TIGR00970 303 ldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyea 377
                                         ++ i++v e+ n++ + erhpy G+lv+tafsGshqdai+kG++a ++ +   ++ w+vpylp+dp+dvgr yea
  lcl|FitnessBrowser__Smeli:SMc02717 313 IERIKEVYEYSNQMVIPERHPYVGELVYTAFSGSHQDAINKGMKAIKQAN---KPTWEVPYLPIDPRDVGRSYEA 384
                                         ********************************************997654...579******************* PP

                           TIGR00970 378 virvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvd 452
                                         +ir+nsqsGkGG+ay+l+ d+G++lpr+lqief + v+ i+d +Gkel sk i + f e+y    ++  ri+ vd
  lcl|FitnessBrowser__Smeli:SMc02717 385 IIRINSQSGKGGIAYILQEDYGINLPRNLQIEFREEVQRITDEEGKELPSKRIHQRFIESYVE--QPGARIKFVD 457
                                         *************************************************************98..5556666655 PP

                           TIGR00970 453 yaveddGt..eskvitavvkikgekkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvel 525
                                         +     G   + +v+ a +  +ge+++ieG G Gp+  +++al+  l ++++vadyseh+l  G++a a +yve+
  lcl|FitnessBrowser__Smeli:SMc02717 458 HHTYPAGEhkGLRVVAAEITDGGETRQIEGKGTGPIDGFINALSIYLGIELSVADYSEHSLQHGSNAAAIAYVEV 532
                                         555554431157999999999****************************************************** PP

                           TIGR00970 526 svrrasdaekatvwGvGiaedvtsaslravlsavnra 562
                                          +         + +GvGi++++ +asl a++sa nr+
  lcl|FitnessBrowser__Smeli:SMc02717 533 EYPGG------KLFGVGINTNIVAASLEAIVSAANRV 563
                                         99765......59**********************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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.23
//
[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