Alignments for a candidate for leuA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Azospirillum brasilense Sp245

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate AZOBR_RS12155 AZOBR_RS12155 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>FitnessBrowser__azobra:AZOBR_RS12155
          Length = 568

 Score =  627 bits (1618), Expect = 0.0
 Identities = 323/601 (53%), Positives = 411/601 (68%), Gaps = 53/601 (8%)

Query: 45  RYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDLLVR 104
           +Y PFA    P++L +R WP+R I++AP+WC+VDLRDGNQALI+PM P RKR MFD L++
Sbjct: 20  KYVPFA----PVKLTDRQWPNRTIEKAPVWCSVDLRDGNQALIEPMGPDRKRAMFDALLK 75

Query: 105 MGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGAPRA 164
           MG+KEIE+GFP+ASQTDFDF REIIE G IPD VTIQVLTQ R ELI RTF+   GA RA
Sbjct: 76  MGFKEIEIGFPAASQTDFDFCREIIEGGKIPDGVTIQVLTQAREELIRRTFEGIKGAKRA 135

Query: 165 IVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYTGTE 224
           IVH YNSTS LQRRVVF  +R  +  IA  G +   + AA++P T+   +YSPES+TGTE
Sbjct: 136 IVHLYNSTSELQRRVVFGLDRQGIVDIAVAGTKLIKQLAAEHPETEIVLQYSPESFTGTE 195

Query: 225 LEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVILSL 284
           LE+A ++C+AV E         +I NLPATVEM+TPN++AD IEW  RN+ NR++ I+SL
Sbjct: 196 LEFALEICEAVMETWGADAANKVILNLPATVEMSTPNIHADQIEWFCRNMKNRDAAIISL 255

Query: 285 HPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQIDFSN 344
           HPHNDRGT VAAAELG  AGADR+EG LFGNGERTGNV ++TL LNL ++GVDP++   +
Sbjct: 256 HPHNDRGTGVAAAELGMLAGADRVEGTLFGNGERTGNVDVITLALNLLTQGVDPELRIDD 315

Query: 345 IDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDVDDM 404
           I+EI R  EYC QLPVH RHPY G+LV+TAFSGSHQDAINKGL A+              
Sbjct: 316 INEIVRVAEYCTQLPVHPRHPYAGELVFTAFSGSHQDAINKGLKALAKSNHGT------- 368

Query: 405 LWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVIQKI 464
            W+VPYLPIDP+D+GR+YEAVIR+NSQSGKGG+AY+++ D+G+ +PRRLQIEFS+ +Q+I
Sbjct: 369 -WEVPYLPIDPQDLGRSYEAVIRINSQSGKGGIAYVLEKDYGIQIPRRLQIEFSKTVQRI 427

Query: 465 AEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKINGVE 524
           A+ T   G E++P ++ +AF  EYL    PL  I    +    + G   +   V  +GV 
Sbjct: 428 ADET---GKELAPADIHNAFKAEYLDIDAPLALIEHSTEPRGPNSGARVLNVVVSRDGVV 484

Query: 525 TEISGSGNGPLAAFVHALAD-VGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIASPAQP 583
           + + GSG GP+ AF+ AL    G D+ V+DY EHA+  G+DAQA AYVE           
Sbjct: 485 STLKGSGKGPIDAFLDALRQGAGIDLHVVDYREHAVGEGEDAQACAYVEVKTN------- 537

Query: 584 GEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSAVNRAA 643
                                           +T++GVG+   I TASLRA+VSA NRA+
Sbjct: 538 ------------------------------DERTLFGVGMDADIVTASLRALVSAANRAS 567

Query: 644 R 644
           R
Sbjct: 568 R 568


Lambda     K      H
   0.317    0.133    0.399 

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: 929
Number of extensions: 36
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: 644
Length of database: 568
Length adjustment: 37
Effective length of query: 607
Effective length of database: 531
Effective search space:   322317
Effective search space used:   322317
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate AZOBR_RS12155 AZOBR_RS12155 (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.14304.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.3e-244  796.2   0.0   9.5e-244  796.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS12155  AZOBR_RS12155 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS12155  AZOBR_RS12155 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.0   0.0  9.5e-244  9.5e-244       3     564 .]      19     568 .]      17     568 .] 0.97

  Alignments for each domain:
  == domain 1  score: 796.0 bits;  conditional E-value: 9.5e-244
                                 TIGR00970   3 kkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfps 71 
                                               +ky pf+++kl++r+wp++ i++ap w+svdlrdGnqali+pm ++rk+ +f+ l+++Gfkeie+gfp+
  lcl|FitnessBrowser__azobra:AZOBR_RS12155  19 EKYVPFAPVKLTDRQWPNRTIEKAPVWCSVDLRDGNQALIEPMGPDRKRAMFDALLKMGFKEIEIGFPA 87 
                                               79******************************************************************* PP

                                 TIGR00970  72 asqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasr 140
                                               asqtdfdf reiie g ipd vtiqvltq+reeli+rt+e ++Gak+aivhlyn+ts+l+r+vvf  +r
  lcl|FitnessBrowser__azobra:AZOBR_RS12155  88 ASQTDFDFCREIIEGGKIPDGVTIQVLTQAREELIRRTFEGIKGAKRAIVHLYNSTSELQRRVVFGLDR 156
                                               ********************************************************************* PP

                                 TIGR00970 141 eevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnl 209
                                               + ++++av g+kl+++l   aa+++et+   +yspesf++telefa+e+ceav e +   +++ +i+nl
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 157 QGIVDIAVAGTKLIKQL---AAEHPETEIVLQYSPESFTGTELEFALEICEAVMETWGADAANKVILNL 222
                                               **********9999987...678899******************************************* PP

                                 TIGR00970 210 patvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertG 278
                                               patve++tpn++ad+ie++++n+ +r+  i+slhphndrGt+vaaaelG+laGadr+eG lfGnGertG
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 223 PATVEMSTPNIHADQIEWFCRNMKNRDAAIISLHPHNDRGTGVAAAELGMLAGADRVEGTLFGNGERTG 291
                                               ********************************************************************* PP

                                 TIGR00970 279 nvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGlda 347
                                               nvd++tlalnl tqGv+p+l   d++ei+rv e+c ++pvh+rhpy+G+lv+tafsGshqdai+kGl+a
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 292 NVDVITLALNLLTQGVDPELRIDDINEIVRVAEYCTQLPVHPRHPYAGELVFTAFSGSHQDAINKGLKA 360
                                               ********************************************************************* PP

                                 TIGR00970 348 ldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkd 416
                                               l k++      w+vpylp+dp+d+gr yeavir+nsqsGkGG+ayvl +d+G+++prrlqiefs+ v+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 361 LAKSNHG---TWEVPYLPIDPQDLGRSYEAVIRINSQSGKGGIAYVLEKDYGIQIPRRLQIEFSKTVQR 426
                                               9988766...9********************************************************** PP

                                 TIGR00970 417 iadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGp 485
                                               iad  Gkel + +i ++fk eyl  + +l  i+  ++    +  +++v++ vv  +g+   ++GsG Gp
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 427 IADETGKELAPADIHNAFKAEYLDIDAPLALIEHSTEPRGPNS-GARVLNVVVSRDGVVSTLKGSGKGP 494
                                               ***********************98888877776666555544.799********************** PP

                                 TIGR00970 486 lsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslra 554
                                               + a++dal++   +d+ v+dy eha+g G+da+a +yve+  + +      t +GvG+++d+ +aslra
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 495 IDAFLDALRQGAGIDLHVVDYREHAVGEGEDAQACAYVEVKTNDE-----RTLFGVGMDADIVTASLRA 558
                                               ***************************************986655.....49***************** PP

                                 TIGR00970 555 vlsavnraar 564
                                               ++sa nra+r
  lcl|FitnessBrowser__azobra:AZOBR_RS12155 559 LVSAANRASR 568
                                               *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (568 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.37
//
[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