Alignments for a candidate for leuA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Klebsiella michiganensis M5al

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate BWI76_RS04680 BWI76_RS04680 2-isopropylmalate synthase

Query= SwissProt::P15875
         (523 letters)



>FitnessBrowser__Koxy:BWI76_RS04680
          Length = 523

 Score =  986 bits (2550), Expect = 0.0
 Identities = 496/523 (94%), Positives = 513/523 (98%)

Query: 1   MSQQVIIFDTTLRDGEQALQASLSAKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60
           MSQQVIIFDTTLRDGEQALQASLS KEKLQIA+ALERMGVDVMEVGFPVSSPGDFESVQT
Sbjct: 1   MSQQVIIFDTTLRDGEQALQASLSVKEKLQIAMALERMGVDVMEVGFPVSSPGDFESVQT 60

Query: 61  IARTIKNSRVCALARCVEKDIDVAAQALKVADAFRIHTFIATSPMHIATKLRSTLDEVIE 120
           IARTIKNSRVCALARCVEKDIDVAA++LKVA+AFRIHTFIATSPMHIATKLRS LDEVIE
Sbjct: 61  IARTIKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSNLDEVIE 120

Query: 121 RAVYMVKRARNYTDDVEFSCEDAGRTPVDDLARVVEAAINAGARTINIPDTVGYTMPFEF 180
           RA+YMVKRARNYTDDVEFSCEDAGRTP+ DLARVVEAAINAGA TINIPDTVGYTMPFEF
Sbjct: 121 RAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYTMPFEF 180

Query: 181 AGIISGLYERVPNIDKAIISVHTHDDLGIAVGNSLAAVHAGARQVEGAMNGIGERAGNCA 240
           A II+GLYE VPNIDKAIISVHTHDDLGIAVGN+LAAVHAGARQVEGAMNGIGERAGNC+
Sbjct: 181 ANIITGLYEHVPNIDKAIISVHTHDDLGIAVGNALAAVHAGARQVEGAMNGIGERAGNCS 240

Query: 241 LEEVIMAIKVRKDIMNVHTNINHHEIWRTSQTVSQICNMPIPANKAIVGSGAFAHSSGIH 300
           LEEVIMAIKVRKDIMNVHT INH EIWRTSQTVSQICNMPIPANKAIVG+GAFAHSSGIH
Sbjct: 241 LEEVIMAIKVRKDIMNVHTRINHQEIWRTSQTVSQICNMPIPANKAIVGTGAFAHSSGIH 300

Query: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMEEMGYKDTDYNMDHLYDAF 360
           QDGVLKNRENYEIMTPESIGLNQ+QLNLTSRSGRAAVKHRMEEMGYK+TDYNMDHLYDAF
Sbjct: 301 QDGVLKNRENYEIMTPESIGLNQVQLNLTSRSGRAAVKHRMEEMGYKETDYNMDHLYDAF 360

Query: 361 LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSDIATASVKLACGEEIKA 420
           LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSDIATASVKLACG+E KA
Sbjct: 361 LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSDIATASVKLACGDETKA 420

Query: 421 EAANGNGPVDAIYQAINRITGYDVELVKYDLNAKGQGKDALGQVDIVVNHHGRRFHGVGL 480
           EAANGNGPVDAIYQAINRITGY++ELVKYDLNAKGQGKDALGQVDIV N++GRRFHGVGL
Sbjct: 421 EAANGNGPVDAIYQAINRITGYEIELVKYDLNAKGQGKDALGQVDIVANYNGRRFHGVGL 480

Query: 481 ATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKENNKETV 523
           ATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKENNKETV
Sbjct: 481 ATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKENNKETV 523


Lambda     K      H
   0.317    0.132    0.372 

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: 26
Number of successful extensions: 1
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: 523
Length of database: 523
Length adjustment: 35
Effective length of query: 488
Effective length of database: 488
Effective search space:   238144
Effective search space used:   238144
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: 52 (24.6 bits)

Align candidate BWI76_RS04680 BWI76_RS04680 (2-isopropylmalate synthase)
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.12155.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.4e-259  846.7  10.2   2.8e-259  846.5  10.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04680  BWI76_RS04680 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04680  BWI76_RS04680 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  846.5  10.2  2.8e-259  2.8e-259       1     494 []       4     497 ..       4     497 .. 1.00

  Alignments for each domain:
  == domain 1  score: 846.5 bits;  conditional E-value: 2.8e-259
                               TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvgla 71 
                                             +v+ifdttlrdGeqa++asl+v+eklqia aler+gvd++e+Gfpvss+gdfe+vq+iar++kn+rv++la
  lcl|FitnessBrowser__Koxy:BWI76_RS04680   4 QVIIFDTTLRDGEQALQASLSVKEKLQIAMALERMGVDVMEVGFPVSSPGDFESVQTIARTIKNSRVCALA 74 
                                             699******************************************************************** PP

                               TIGR00973  72 ravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagr 142
                                             r+vekdid+aae+lk+ae++rihtfiats++h+++kl+++ dev+er++++vk+a+n++ddvefs+edagr
  lcl|FitnessBrowser__Koxy:BWI76_RS04680  75 RCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSNLDEVIERAIYMVKRARNYTDDVEFSCEDAGR 145
                                             *********************************************************************** PP

                               TIGR00973 143 teleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavansla 213
                                             t++++larvveaai+aGattiniPdtvGy++P e++++i +l+e+vPnidkai+svh+hddlG+av+n+la
  lcl|FitnessBrowser__Koxy:BWI76_RS04680 146 TPIADLARVVEAAINAGATTINIPDTVGYTMPFEFANIITGLYEHVPNIDKAIISVHTHDDLGIAVGNALA 216
                                             *********************************************************************** PP

                               TIGR00973 214 avknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkai 284
                                             av++Garqve+++nGiGeraGn++leev+ma+kvrkd++nv+t in++ei+rts+ vs++++m++++nkai
  lcl|FitnessBrowser__Koxy:BWI76_RS04680 217 AVHAGARQVEGAMNGIGERAGNCSLEEVIMAIKVRKDIMNVHTRINHQEIWRTSQTVSQICNMPIPANKAI 287
                                             *********************************************************************** PP

                               TIGR00973 285 vGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfe 355
                                             vG +afah+sGihqdGvlkn+e+yei++pesiGl++ +l+l++rsGraa+k+r+ee+G+k++++++d+l++
  lcl|FitnessBrowser__Koxy:BWI76_RS04680 288 VGTGAFAHSSGIHQDGVLKNRENYEIMTPESIGLNQVQLNLTSRSGRAAVKHRMEEMGYKETDYNMDHLYD 358
                                             *********************************************************************** PP

                               TIGR00973 356 kfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpv 426
                                             +f++ladkk++vfd+dleal++++++qee e+++l++++vqsg+++++ta vkl++ +e k++aa+GnGpv
  lcl|FitnessBrowser__Koxy:BWI76_RS04680 359 AFLKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSDIATASVKLACGDETKAEAANGNGPV 429
                                             ********************************************************9999*********** PP

                               TIGR00973 427 davykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                             da+y+ai++i+++e++l++y ++akg+gkdalg+v++v+++ng++++G+g+atdive+saka+v++ln
  lcl|FitnessBrowser__Koxy:BWI76_RS04680 430 DAIYQAINRITGYEIELVKYDLNAKGQGKDALGQVDIVANYNGRRFHGVGLATDIVESSAKAMVHVLN 497
                                             ******************************************************************98 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: 11.16
//
[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