Alignments for a candidate for leuA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Shewanella oneidensis MR-1

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate 203317 SO4236 2-isopropylmalate synthase (NCBI ptt file)

Query= SwissProt::P15875
         (523 letters)



>FitnessBrowser__MR1:203317
          Length = 522

 Score =  685 bits (1767), Expect = 0.0
 Identities = 348/518 (67%), Positives = 414/518 (79%), Gaps = 1/518 (0%)

Query: 1   MSQQVIIFDTTLRDGEQALQASLSAKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60
           MS +VIIFDTTLRDGEQAL ASLS KEKLQIA+ALER+GVDVMEVGFPVSSPGDFESVQT
Sbjct: 1   MSNRVIIFDTTLRDGEQALAASLSVKEKLQIAMALERLGVDVMEVGFPVSSPGDFESVQT 60

Query: 61  IARTIKNSRVCALARCVEKDIDVAAQALKVADAFRIHTFIATSPMHIATKLRSTLDEVIE 120
           IARTIKNSRVCAL+R +EKDID AAQAL VA+ FRIHTFI+TS +H+ +KL+ + ++V+E
Sbjct: 61  IARTIKNSRVCALSRALEKDIDAAAQALSVAEQFRIHTFISTSTIHVESKLKRSFEQVLE 120

Query: 121 RAVYMVKRARNYTDDVEFSCEDAGRTPVDDLARVVEAAINAGARTINIPDTVGYTMPFEF 180
            AV  VK AR +TDDVEFSCEDAGRTP+D+L R+VEAAI+AGARTINIPDTVGYT+P EF
Sbjct: 121 MAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAIHAGARTINIPDTVGYTVPSEF 180

Query: 181 AGIISGLYERVPNIDKAIISVHTHDDLGIAVGNSLAAVHAGARQVEGAMNGIGERAGNCA 240
             II  L+ RVPNID+AIISVH HDDLG++V NS+ AV  GARQ+E  MNGIGERAGNC+
Sbjct: 181 GSIIQTLFNRVPNIDQAIISVHCHDDLGLSVANSITAVQHGARQIECTMNGIGERAGNCS 240

Query: 241 LEEVIMAIKVRKDIMNVHTNINHHEIWRTSQTVSQICNMPIPANKAIVGSGAFAHSSGIH 300
           LEE+ M +  RK+++   T IN  EI RTS  VSQ+CNMPI +NKAIVG+ AF HSSGIH
Sbjct: 241 LEEIAMILATRKNLLGFETGINAKEIHRTSNLVSQLCNMPIQSNKAIVGANAFTHSSGIH 300

Query: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMEEMGYKDTDYNMDHLYDAF 360
           QDG+LK +  YEIMTPESIGLN+  LN+TSRSGR  +KHRMEEMGY   DYN+D LY+ F
Sbjct: 301 QDGMLKAQNTYEIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYSSQDYNLDALYEQF 360

Query: 361 LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSD-IATASVKLACGEEIK 419
           L LADKKGQVFDYDLEALAFI  Q  E   ++L    VQS S++ +ATA+V++  G EIK
Sbjct: 361 LHLADKKGQVFDYDLEALAFIEAQAAEDNFYQLRQLVVQSDSTEGVATATVRIEVGGEIK 420

Query: 420 AEAANGNGPVDAIYQAINRITGYDVELVKYDLNAKGQGKDALGQVDIVVNHHGRRFHGVG 479
            EAA GNGPVDA Y AI R T   ++++ Y L AKG G+DALGQVDI   +H + FHGVG
Sbjct: 421 TEAATGNGPVDAAYNAIARATDRRIDIISYKLGAKGVGQDALGQVDITAVYHEQNFHGVG 480

Query: 480 LATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKE 517
           LATD+VE+SA+A+VHV+N   RA +V    Q   +N+E
Sbjct: 481 LATDVVEASARALVHVMNLTCRADKVADYKQNMHKNRE 518


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: 752
Number of extensions: 23
Number of successful extensions: 2
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: 522
Length adjustment: 35
Effective length of query: 488
Effective length of database: 487
Effective search space:   237656
Effective search space used:   237656
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 203317 SO4236 (2-isopropylmalate synthase (NCBI ptt file))
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.20762.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.7e-240  784.5  10.3   1.9e-240  784.4  10.3    1.0  1  lcl|FitnessBrowser__MR1:203317  SO4236 2-isopropylmalate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203317  SO4236 2-isopropylmalate synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  784.4  10.3  1.9e-240  1.9e-240       1     494 []       4     498 ..       4     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 784.4 bits;  conditional E-value: 1.9e-240
                       TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdid 79 
                                     rv+ifdttlrdGeqa+ asl+v+eklqia alerlgvd++e+Gfpvss+gdfe+vq+iar++kn+rv++l+ra+ekdid
  lcl|FitnessBrowser__MR1:203317   4 RVIIFDTTLRDGEQALAASLSVKEKLQIAMALERLGVDVMEVGFPVSSPGDFESVQTIARTIKNSRVCALSRALEKDID 82 
                                     79***************************************************************************** PP

                       TIGR00973  80 aaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaaiea 158
                                     aaa+al +ae++rihtfi+ts ih+e klk+++++vle++v avkya+ f+ddvefs+edagrt++++l+r+veaai+a
  lcl|FitnessBrowser__MR1:203317  83 AAAQALSVAEQFRIHTFISTSTIHVESKLKRSFEQVLEMAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAIHA 161
                                     ******************************************************************************* PP

                       TIGR00973 159 GattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGeraGnaa 237
                                     Ga tiniPdtvGy++P+e+g++i++l ++vPnid+ai+svhchddlGl+vans++av++Garq+ect+nGiGeraGn++
  lcl|FitnessBrowser__MR1:203317 162 GARTINIPDTVGYTVPSEFGSIIQTLFNRVPNIDQAIISVHCHDDLGLSVANSITAVQHGARQIECTMNGIGERAGNCS 240
                                     ******************************************************************************* PP

                       TIGR00973 238 leevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesi 316
                                     lee++m+l +rk++l+ etgin kei+rts+lvs+l++m++q+nkaivG+naf h+sGihqdG+lk ++tyei++pesi
  lcl|FitnessBrowser__MR1:203317 241 LEEIAMILATRKNLLGFETGINAKEIHRTSNLVSQLCNMPIQSNKAIVGANAFTHSSGIHQDGMLKAQNTYEIMTPESI 319
                                     ******************************************************************************* PP

                       TIGR00973 317 GlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqv 395
                                     Gl++++l++++rsGr+ +k+r+ee+G+  ++++ld l+e+f++ladkk++vfd+dleal+++e +  e++ ++l +l v
  lcl|FitnessBrowser__MR1:203317 320 GLNRNNLNMTSRSGRHVIKHRMEEMGYSSQDYNLDALYEQFLHLADKKGQVFDYDLEALAFIEAQAAEDNFYQLRQLVV 398
                                     ******************************************************************************* PP

                       TIGR00973 396 qsge.esvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkys 473
                                     qs + e v+tatv+++v ge k++aatGnGpvda y+ai ++++  ++++ y++ akg g+dalg+v++++ +++++++
  lcl|FitnessBrowser__MR1:203317 399 QSDStEGVATATVRIEVGGEIKTEAATGNGPVDAAYNAIARATDRRIDIISYKLGAKGVGQDALGQVDITAVYHEQNFH 477
                                     9965167************************************************************************ PP

                       TIGR00973 474 Grgvatdiveasakayvnaln 494
                                     G+g+atd+veasa+a+v+++n
  lcl|FitnessBrowser__MR1:203317 478 GVGLATDVVEASARALVHVMN 498
                                     *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (522 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: 6.85
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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