Alignments for a candidate for ilvI in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Synechococcus elongatus PCC 7942

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Synpcc7942_0139 Synpcc7942_0139 acetolactate synthase 3 catalytic subunit

Query= BRENDA::P9WG41
         (618 letters)



>FitnessBrowser__SynE:Synpcc7942_0139
          Length = 612

 Score =  555 bits (1430), Expect = e-162
 Identities = 305/573 (53%), Positives = 380/573 (66%), Gaps = 17/573 (2%)

Query: 36  QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSK---KLRHVLVRHEQGAGHAA 92
           Q+ TGA A+I SL + GV  IFG PGGA+LP+YD L  ++   +++H+LVRHEQGA HAA
Sbjct: 10  QRATGAYALIDSLCQHGVKHIFGYPGGAILPIYDELHRAEAAGRVQHILVRHEQGAVHAA 69

Query: 93  SGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADI 152
             Y+  TG VGVC ATSGPGATNLVT +A AQMDSIP+V +TGQV R  IGTDAFQE DI
Sbjct: 70  DAYSRATGEVGVCFATSGPGATNLVTGIATAQMDSIPMVVVTGQVPRTAIGTDAFQETDI 129

Query: 153 SGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPP-- 210
            GIT+PI KH+++VR   D+ R++AEAFHIA SGRPG VL+D+PKDV  G   F + P  
Sbjct: 130 YGITLPIVKHSYVVRDPRDMARIVAEAFHIAQSGRPGPVLIDVPKDV--GTEEFDYVPVA 187

Query: 211 --RMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIP 268
              + LPGY+P T+ + RQ+ +A  L+  AR+P+LYVGGG I   A  +LR  AE   +P
Sbjct: 188 PGDIRLPGYRPTTRGNPRQIAQAIALVKVARRPLLYVGGGAITAGAHAELRAFAERFQLP 247

Query: 269 VVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAP 328
           V TTLM +GAF + H   LGM GMHGT  A  A+   DLLIA+G RFDDRVTGKLD FA 
Sbjct: 248 VTTTLMGKGAFDERHPLALGMLGMHGTAYANFAVSECDLLIAVGARFDDRVTGKLDEFAS 307

Query: 329 EAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHH-HIPGTIEMADWWAYLNG 387
           +A+VIH DIDPAE+GKNR  +VPIVGDV+ V+ EL+A                W   +  
Sbjct: 308 KAQVIHVDIDPAEVGKNRVPEVPIVGDVRQVLNELLARAEEQISADDATRTQPWLDRIAY 367

Query: 388 VRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWL 447
            ++ YPL   P     LSP+ VI  LGE A PDA F   VGQHQMWAAQFI+   PR W+
Sbjct: 368 WKREYPLQI-PYYADVLSPQQVIHSLGE-AAPDAYFTTDVGQHQMWAAQFIK-NGPRRWI 424

Query: 448 NSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINN 507
           +S GLGTMGF +PAAMGA++ALP   V  + GD    M  QEL T A   IP+KV ++NN
Sbjct: 425 SSAGLGTMGFGMPAAMGAQMALPDDTVICVAGDASILMNIQELGTLAQYNIPIKVVVVNN 484

Query: 508 GNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQA 567
           G  GMVRQWQ  FY ERYS +++      +PDFVKLAEA G  G+R    +++   I + 
Sbjct: 485 GWQGMVRQWQEAFYDERYSNSNM---ERGMPDFVKLAEAFGIKGMRVSHPDELQAAIAEM 541

Query: 568 RAINDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
            A  D PV +D IV  D   +PMV +G SN ++
Sbjct: 542 LAF-DGPVFLDAIVKRDENCYPMVPSGHSNAQM 573


Lambda     K      H
   0.319    0.136    0.414 

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: 1138
Number of extensions: 55
Number of successful extensions: 7
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: 618
Length of database: 612
Length adjustment: 37
Effective length of query: 581
Effective length of database: 575
Effective search space:   334075
Effective search space used:   334075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate Synpcc7942_0139 Synpcc7942_0139 (acetolactate synthase 3 catalytic subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.3830.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-266  869.9   0.1   4.1e-266  869.7   0.1    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0139  Synpcc7942_0139 acetolactate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0139  Synpcc7942_0139 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  869.7   0.1  4.1e-266  4.1e-266       2     555 ..      13     575 ..      12     577 .. 0.98

  Alignments for each domain:
  == domain 1  score: 869.7 bits;  conditional E-value: 4.1e-266
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly....dselehilvrheqaaahaadGyarasGkvGv 66 
                                               +ga++l++sl ++gv+++fGyPGGa+lpiyd+l+    ++ ++hilvrheq+a+haad y+ra+G+vGv
  lcl|FitnessBrowser__SynE:Synpcc7942_0139  13 TGAYALIDSLCQHGVKHIFGYPGGAILPIYDELHraeaAGRVQHILVRHEQGAVHAADAYSRATGEVGV 81 
                                               79********************************9887789**************************** PP

                                 TIGR00118  67 vlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135
                                               ++atsGPGatnlvtgiata +ds+P+vv+tGqv++++iG+dafqe di Gitlp++khs++v++++d++
  lcl|FitnessBrowser__SynE:Synpcc7942_0139  82 CFATSGPGATNLVTGIATAQMDSIPMVVVTGQVPRTAIGTDAFQETDIYGITLPIVKHSYVVRDPRDMA 150
                                               ********************************************************************* PP

                                 TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakk 202
                                               +i+ eaf+ia++GrPGPvl+d+Pkdv ++e+++      ++ lpgy+pt++g+++qi++a+ l++ a++
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 151 RIVAEAFHIAQSGRPGPVLIDVPKDVGTEEFDYVPVapGDIRLPGYRPTTRGNPRQIAQAIALVKVARR 219
                                               ********************************9877679****************************** PP

                                 TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                               P+l+vGgG+i+a+a++el+ +aer+++pvtttl+G+Gaf+e hplalgmlGmhGt++an+avse+dlli
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 220 PLLYVGGGAITAGAHAELRAFAERFQLPVTTTLMGKGAFDERHPLALGMLGMHGTAYANFAVSECDLLI 288
                                               ********************************************************************* PP

                                 TIGR00118 272 avGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekke 336
                                               avGarfddrvtg+l++fa++a++ih+didPae+gkn+  ++pivGd+++vl+ell++++e+    + + 
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 289 AVGARFDDRVTGKLDEFASKAQVIHVDIDPAEVGKNRVPEVPIVGDVRQVLNELLARAEEQisadDATR 357
                                               *********************************************************999988764555 PP

                                 TIGR00118 337 ke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                               ++ Wl++i+ wk+ey+l++ ++ + + Pq+vi++l + ++d a+ ttdvGqhqmwaaqf k+  pr++i
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 358 TQpWLDRIAYWKREYPLQIPYYADVLSPQQVIHSLGEAAPD-AYFTTDVGQHQMWAAQFIKNG-PRRWI 424
                                               567*************************************6.******************998.***** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +s+GlGtmGfG+Paa+Ga++a p++tv++v+Gd+s+ mn+qel t+++y+ip+k+v++nn ++Gmv+qW
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 425 SSAGLGTMGFGMPAAMGAQMALPDDTVICVAGDASILMNIQELGTLAQYNIPIKVVVVNNGWQGMVRQW 493
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               qe fy+erys+++++ ++pdfvklaea+G+kg+r+++p+el+++++e+l+ ++pv+ld  v+++e+++P
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 494 QEAFYDERYSNSNMERGMPDFVKLAEAFGIKGMRVSHPDELQAAIAEMLAFDGPVFLDAIVKRDENCYP 562
                                               ********************************************************************* PP

                                 TIGR00118 543 mvapGagldelve 555
                                               mv++G++++++++
  lcl|FitnessBrowser__SynE:Synpcc7942_0139 563 MVPSGHSNAQMLG 575
                                               **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (612 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: 00:00:00.03
# Mc/sec: 8.91
//
[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