Alignments for a candidate for leuA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Synechococcus elongatus PCC 7942

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate Synpcc7942_1410 Synpcc7942_1410 2-isopropylmalate synthase

Query= BRENDA::Q2RAP8
         (635 letters)



>FitnessBrowser__SynE:Synpcc7942_1410
          Length = 540

 Score =  503 bits (1296), Expect = e-147
 Identities = 284/533 (53%), Positives = 359/533 (67%), Gaps = 33/533 (6%)

Query: 91  VRIFDTTLRDGEQSPGATMTSAEKLVVARQLARLGVDIIEAGFPASSPDDLDAVRSIAIE 150
           + IFDTTLRDGEQSPGA++   EKL +ARQLARL VDIIEAGF  +SP D +AV+ IA E
Sbjct: 10  ILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDFEAVQRIAAE 69

Query: 151 VGNTPVGEDGHVPVICGLSRCNKRDIDAAWEAVRHARRPRIHTFIATSEIHMQHKLRKTP 210
           VG TP G     P IC L+R  ++DI AA EA+  A + RIHTFIATS+IH+++KL+KT 
Sbjct: 70  VG-TPDG-----PTICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKLKKTR 123

Query: 211 EQVVAIAKEMVAYARSLGCPDVEFSPEDAGRSNREFLYHILEEVIKAGATTLNIPDTVGY 270
            +V+A+  EMV YA SL   DVEFSPEDAGRS+ EFLY  LE  I AGA T+NIPDTVGY
Sbjct: 124 AEVLAVIPEMVGYAASL-VDDVEFSPEDAGRSDPEFLYECLEAAIAAGAKTINIPDTVGY 182

Query: 271 TLPYEFGKLIADIKANTPGIENAIISTHCQNDLGLATANTLAGAHAGARQLEVTINGIGE 330
           T P EFG LI  IK N   I+ AIIS H  NDLGLA AN L     GARQLE TINGIGE
Sbjct: 183 TTPSEFGALIGGIKQNVCNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGIGE 242

Query: 331 RAGNASLEEVVMAIKCRRELLGGL----------YTGINTQHITMSSKMVQEHSGLHVQP 380
           RAGNA+LEE+VMA+  RR+                T +NT+ I  +S++V   +G+ VQP
Sbjct: 243 RAGNAALEELVMALHVRRQYFNPFLGRAADSEAPLTQVNTREIYKTSRLVSNLTGMLVQP 302

Query: 381 HKAIVGANAFAHESGIHQDGMLKYKGTYEIISPDDIGLTRANEFGIVLGKLSGRHAVRSK 440
           +KAIVGANAFAHESGIHQDG+LK K TYEI+  + IGL+      I LGKLSGR+A R++
Sbjct: 303 NKAIVGANAFAHESGIHQDGVLKNKLTYEIVDAETIGLSTNR---ITLGKLSGRNAFRTR 359

Query: 441 LVELGYEITDKEFEDFFKRYKEVAEKKKRVTDEDIEALLSDEIFQPKVFWSLADVQATCG 500
           L ELGY++ + +    F R+KE+A+KK+ VTD D+EA+++DE  Q    + L  VQ + G
Sbjct: 360 LQELGYDLGEDDLNRAFLRFKELADKKREVTDRDLEAIVNDETQQAPELFKLELVQVSAG 419

Query: 501 TLGLSTATVKLIGPDGEEKIACAVGTGPVDAAYKAVDDIIQIPTVLREYSMTSVTEGIDA 560
                TATV L  P+GEE    A+GTGPVDA Y+A++ ++ IP  L E+S+ SVT GIDA
Sbjct: 420 DHARPTATVTLRTPEGEELTDAAIGTGPVDAIYRAINRVVNIPNELIEFSVKSVTAGIDA 479

Query: 561 IATTRVVVTGDVSDSKHALTGHSFSRAFSGSGAALDIVVSSVRAYLSALNKMS 613
           I    + +  +              R FSG  A  DI+V+S +AY+ ALN+++
Sbjct: 480 IGEVTIRLRHE-------------DRIFSGHSANTDILVASAQAYIHALNRLA 519


Lambda     K      H
   0.316    0.131    0.373 

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: 791
Number of extensions: 30
Number of successful extensions: 8
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: 635
Length of database: 540
Length adjustment: 37
Effective length of query: 598
Effective length of database: 503
Effective search space:   300794
Effective search space used:   300794
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 Synpcc7942_1410 Synpcc7942_1410 (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.26747.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-239  779.5   1.3   6.6e-239  779.3   1.3    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1410  Synpcc7942_1410 2-isopropylmalat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1410  Synpcc7942_1410 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  779.3   1.3  6.6e-239  6.6e-239       1     494 []       9     516 ..       9     516 .. 0.99

  Alignments for each domain:
  == domain 1  score: 779.3 bits;  conditional E-value: 6.6e-239
                                 TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknar... 66 
                                               r+lifdttlrdGeq+pgasl++eekl+ia++l+rl+vdiieaGf+++s+gdfeavq+ia ev ++    
  lcl|FitnessBrowser__SynE:Synpcc7942_1410   9 RILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDFEAVQRIAAEVGTPDgpt 77 
                                               79************************************************************9876666 PP

                                 TIGR00973  67 vvglaravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvef 135
                                               +++lara+ +di+aaaeal pa+k rihtfiatsdihle+klkkt++evl++i ++v ya ++vddvef
  lcl|FitnessBrowser__SynE:Synpcc7942_1410  78 ICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKLKKTRAEVLAVIPEMVGYAASLVDDVEF 146
                                               ********************************************************************* PP

                                 TIGR00973 136 saedagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddl 204
                                               s+edagr++ efl++ +eaai aGa tiniPdtvGy++P+e+g+li ++k+nv nid+ai+svh+h+dl
  lcl|FitnessBrowser__SynE:Synpcc7942_1410 147 SPEDAGRSDPEFLYECLEAAIAAGAKTINIPDTVGYTTPSEFGALIGGIKQNVCNIDQAIISVHGHNDL 215
                                               ********************************************************************* PP

                                 TIGR00973 205 GlavanslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetg...........intke 262
                                               Glavan+l+avknGarq+ectinGiGeraGnaalee+vmal+vr++++n ++g           +nt+e
  lcl|FitnessBrowser__SynE:Synpcc7942_1410 216 GLAVANFLEAVKNGARQLECTINGIGERAGNAALEELVMALHVRRQYFNPFLGraadseapltqVNTRE 284
                                               ***************************************************9999************** PP

                                 TIGR00973 263 iyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGr 331
                                               iy+tsrlvs+ltgmlvq+nkaivG+nafahesGihqdGvlknk tyei+++e+iGl+++++ lgk sGr
  lcl|FitnessBrowser__SynE:Synpcc7942_1410 285 IYKTSRLVSNLTGMLVQPNKAIVGANAFAHESGIHQDGVLKNKLTYEIVDAETIGLSTNRITLGKLSGR 353
                                               ********************************************************************* PP

                                 TIGR00973 332 aalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgee 400
                                               +a+++rl+elG++l e++l+++f +fkeladkk+ev+d dlea+v++e++q +e  +kle +qv++g++
  lcl|FitnessBrowser__SynE:Synpcc7942_1410 354 NAFRTRLQELGYDLGEDDLNRAFLRFKELADKKREVTDRDLEAIVNDETQQAPEL-FKLELVQVSAGDH 421
                                               **************************************************88887.************* PP

                                 TIGR00973 401 svptatvklkvk.geekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvleln 468
                                                 ptatv+l+++ gee ++aa+G+Gpvda+y+ai+++++++++l+e+s+++++ g da+gev+++l+++
  lcl|FitnessBrowser__SynE:Synpcc7942_1410 422 ARPTATVTLRTPeGEELTDAAIGTGPVDAIYRAINRVVNIPNELIEFSVKSVTAGIDAIGEVTIRLRHE 490
                                               ***********98999***************************************************** PP

                                 TIGR00973 469 gkkysGrgvatdiveasakayvnaln 494
                                               ++ +sG++++tdi+ asa+ay++aln
  lcl|FitnessBrowser__SynE:Synpcc7942_1410 491 DRIFSGHSANTDILVASAQAYIHALN 516
                                               *************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (540 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.04
//
[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