Alignments for a candidate for leuA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Herbaspirillum seropedicae SmR1

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate HSERO_RS17185 HSERO_RS17185 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__HerbieS:HSERO_RS17185
          Length = 567

 Score =  618 bits (1593), Expect = 0.0
 Identities = 318/581 (54%), Positives = 402/581 (69%), Gaps = 25/581 (4%)

Query: 35  SMPVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMF 94
           S P  +Y PF      I LPDRTWP K I   P W + DLRDGNQALI+PM+ ERK R F
Sbjct: 4   SNPAAKYRPFPA----IDLPDRTWPSKVINTPPIWMSTDLRDGNQALIEPMNAERKLRFF 59

Query: 95  ELLVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACE 154
           ELL++ G KEIEVGFPSASQTDFDFVR++I +  IPDDVTI VL Q+RE LIRRT E+ E
Sbjct: 60  ELLLKTGLKEIEVGFPSASQTDFDFVRKLIVENRIPDDVTIIVLTQSREELIRRTIESLE 119

Query: 155 GAKNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPES 214
           GAK  IVH YNS +   R +VF M + ++K +A     L+K +    P T WR++YSPES
Sbjct: 120 GAKKAIVHLYNSVAPAFRKIVFNMSREEIKNIAVTGTRLVKELTDARPGTEWRFEYSPES 179

Query: 215 FTGTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDS 274
           F+ TE++++KE+ DAV E    +PE  +I+NLPSTVE  TPNVYAD IEWM RNL  R S
Sbjct: 180 FSTTELDFSKEICDAVCETWGASPERKVILNLPSTVECATPNVYADQIEWMCRNLKDRAS 239

Query: 275 IILSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQ 334
            I+S+HPHNDRGT V +AEL  MAGADR+EGCLFGNGERTGNV LVTLALN+ TQGV+P 
Sbjct: 240 TIISVHPHNDRGTAVASAELAVMAGADRVEGCLFGNGERTGNVDLVTLALNLYTQGVNPG 299

Query: 335 LDFTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGAS 394
           LDF+DI  +R  VE CNQ+ V  RHPY GDLVFTAFSGSHQDA+ KG     AK QP   
Sbjct: 300 LDFSDIDVVRQVVEECNQIPVHPRHPYVGDLVFTAFSGSHQDAIKKGF----AKQQP--- 352

Query: 395 STEVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRS 454
                     D  WEVPYLPIDP D+GR Y+AVIRVNSQSGKGG+AY+++ ++GL +PR 
Sbjct: 353 ----------DAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQEYGLALPRR 402

Query: 455 MQVEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASIT 514
           +Q+EFS  +Q   DA G E+ +  +  IF  EYLER  P    A R+    ++ E  +I 
Sbjct: 403 LQIEFSRAIQREADATGKEIAASDIHAIFQREYLERVEPYVYRAHRMSEDSSKAESINIE 462

Query: 515 AELIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEV 574
            +++ NG+ VTV G GNGP+ A+ +A   LG+D+++ ++++HA  +G DA+AA+Y+   +
Sbjct: 463 VDIVRNGQPVTVRGSGNGPIDAFVHA---LGLDIKLMDFHEHAIGAGADAKAASYIELRL 519

Query: 575 NGRKV-WGVGIAGSITYASLKAVTSAVNRALDVNHEAVLAG 614
           N     +GVGI  +I  AS KAV SAVNR + ++  A  AG
Sbjct: 520 NEAPTGFGVGIDANIVTASFKAVLSAVNRQIAISESANQAG 560


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: 944
Number of extensions: 30
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: 616
Length of database: 567
Length adjustment: 37
Effective length of query: 579
Effective length of database: 530
Effective search space:   306870
Effective search space used:   306870
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 HSERO_RS17185 HSERO_RS17185 (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.3417.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.3e-247  808.8   0.0   1.5e-247  808.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS17185  HSERO_RS17185 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS17185  HSERO_RS17185 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.6   0.0  1.5e-247  1.5e-247       1     563 [.       6     550 ..       6     551 .. 0.96

  Alignments for each domain:
  == domain 1  score: 808.6 bits;  conditional E-value: 1.5e-247
                                  TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievg 68 
                                                p+ ky+pf ai l++r+wp kvi+  p w+s+dlrdGnqali+pm++erk r+f+ll++ G keievg
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185   6 PAAKYRPFPAIDLPDRTWPSKVINTPPIWMSTDLRDGNQALIEPMNAERKLRFFELLLKTGLKEIEVG 73 
                                                889***************************************************************** PP

                                  TIGR00970  69 fpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvf 136
                                                fpsasqtdfdfvr++i ++ ipddvti vltqsreeli+rt+e+l+Gakkaivhlyn++++ fr++vf
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185  74 FPSASQTDFDFVRKLIVENRIPDDVTIIVLTQSREELIRRTIESLEGAKKAIVHLYNSVAPAFRKIVF 141
                                                **************99999************************************************* PP

                                  TIGR00970 137 rasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerp 204
                                                ++sree+ ++av g++lv++l++    +++t+w+feyspesfs tel+f++e+c+av e +  ++er 
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 142 NMSREEIKNIAVTGTRLVKELTDA---RPGTEWRFEYSPESFSTTELDFSKEICDAVCETWGASPERK 206
                                                *******************99975...689************************************** PP

                                  TIGR00970 205 iifnlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfG 272
                                                +i+nlp+tve atpnvyad+ie++++n+ +r + i+s+hphndrGtava+ael ++aGadr+eGclfG
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 207 VILNLPSTVECATPNVYADQIEWMCRNLKDRASTIISVHPHNDRGTAVASAELAVMAGADRVEGCLFG 274
                                                ******************************************************************** PP

                                  TIGR00970 273 nGertGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqda 340
                                                nGertGnvdlvtlalnlytqGv+p ldfsd+d +++vve+cn+ipvh+rhpy Gdlv+tafsGshqda
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 275 NGERTGNVDLVTLALNLYTQGVNPGLDFSDIDVVRQVVEECNQIPVHPRHPYVGDLVFTAFSGSHQDA 342
                                                ******************************************************************** PP

                                  TIGR00970 341 ikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqi 408
                                                ikkG+       ++ d++w+vpylp+dp d+gr y+avirvnsqsGkGG+ay+l +++Gl lprrlqi
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 343 IKKGFAK-----QQPDAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQEYGLALPRRLQI 405
                                                ****964.....456889************************************************** PP

                                  TIGR00970 409 efssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvki..kge 474
                                                efs++++  ad+ Gke+ +++i  +f+ eyl  ve++  ++ +    ++d +++++i+  v+i  +g+
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 406 EFSRAIQREADATGKEIAASDIHAIFQREYLERVEPYV-YRAHRM--SEDSSKAESINIEVDIvrNGQ 470
                                                *******************************9888774.455544..445555666666666644899 PP

                                  TIGR00970 475 kkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvG 542
                                                 + + GsGnGp+ a+v+al     +d++++d+ eha+g+G dakaasy+el +++a      t +GvG
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 471 PVTVRGSGNGPIDAFVHALG----LDIKLMDFHEHAIGAGADAKAASYIELRLNEAP-----TGFGVG 529
                                                99****************95....7889************************99887.....89**** PP

                                  TIGR00970 543 iaedvtsaslravlsavnraa 563
                                                i++++ +as++avlsavnr +
  lcl|FitnessBrowser__HerbieS:HSERO_RS17185 530 IDANIVTASFKAVLSAVNRQI 550
                                                ******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (567 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: 00:00:00.09
# Mc/sec: 3.41
//
[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