GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Sinorhizobium meliloti 1021

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate SMc02896 SMc02896 branched-chain amino acid aminotransferase

Query= reanno::Cup4G11:RR42_RS25890
         (363 letters)



>FitnessBrowser__Smeli:SMc02896
          Length = 365

 Score =  446 bits (1148), Expect = e-130
 Identities = 215/356 (60%), Positives = 266/356 (74%), Gaps = 1/356 (0%)

Query: 4   QTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPFSID 63
           + TF  E NP  +  + RDAL+ +P FGRVFTDHM TI + EG+GW DAK+  RK F +D
Sbjct: 6   EQTFLFEQNPTRVANSERDALLANPGFGRVFTDHMATIRYSEGRGWHDAKIGPRKAFDLD 65

Query: 64  PACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLEAIE 123
           P+  VLHY QEIFEGMKAYR  DG  TLFRP  NARRF+ SA R+AM  LPE LF++++ 
Sbjct: 66  PSTLVLHYAQEIFEGMKAYRLPDGGATLFRPDANARRFRNSALRLAMAPLPEELFVQSVR 125

Query: 124 QLVRIDQAWVPHGSGS-LYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKAVS 182
           +LVRID+ W+P G G+ LYLRPFM A EV LG+KP++E+++CVIA  VG YFKGG  A++
Sbjct: 126 ELVRIDRDWIPAGEGAALYLRPFMIATEVLLGVKPSAEYLYCVIASSVGSYFKGGAPAIT 185

Query: 183 VWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGGMN 242
           +WVSENYTRAAPGGTGEAKCGGNYA SL AQ EA   GC+QVVFLDA E R+VEELGGMN
Sbjct: 186 IWVSENYTRAAPGGTGEAKCGGNYAASLAAQAEAMQEGCEQVVFLDAVERRFVEELGGMN 245

Query: 243 IFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRLAE 302
           +FF   DG+L TPPL+G+ILPGITR S+I LAR+MG+ V E  Y+  +W+ADA+SGRL E
Sbjct: 246 VFFGFRDGSLQTPPLTGTILPGITRDSLITLARDMGLTVREEPYAIDQWQADAESGRLTE 305

Query: 303 AFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWV 358
           AF CGTAA +  IG+V+     F IG+G AG     L+  L++IQ  +A  P GW+
Sbjct: 306 AFACGTAAVVTPIGKVKGREHSFTIGDGGAGPVASRLKSALLDIQNGRAPDPHGWL 361


Lambda     K      H
   0.321    0.135    0.415 

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: 452
Number of extensions: 18
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: 363
Length of database: 365
Length adjustment: 29
Effective length of query: 334
Effective length of database: 336
Effective search space:   112224
Effective search space used:   112224
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate SMc02896 SMc02896 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01123.hmm
# target sequence database:        /tmp/gapView.12953.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-125  404.7   0.0   1.3e-125  404.5   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02896  SMc02896 branched-chain amino ac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02896  SMc02896 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.5   0.0  1.3e-125  1.3e-125       1     311 [.      51     362 ..      51     364 .. 0.99

  Alignments for each domain:
  == domain 1  score: 404.5 bits;  conditional E-value: 1.3e-125
                           TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealk 75 
                                         W++a++ + +++ ld+++ vlhY+qe+feG+kayR  dG ++lfRpdana+R+r+sa rl++  l+eelf+++++
  lcl|FitnessBrowser__Smeli:SMc02896  51 WHDAKIGPRKAFDLDPSTLVLHYAQEIFEGMKAYRLPDGGATLFRPDANARRFRNSALRLAMAPLPEELFVQSVR 125
                                         *************************************************************************** PP

                           TIGR01123  76 qlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkG 150
                                         +lv++d+dw+p a+ +a+LYlRPf+iate  lGvk++ eyl++v+as vG+Yfkgg   ++i+v+++y+Raap+G
  lcl|FitnessBrowser__Smeli:SMc02896 126 ELVRIDRDWIP-AGEGAALYLRPFMIATEVLLGVKPSAEYLYCVIASSVGSYFKGGAPAITIWVSENYTRAAPGG 199
                                         ***********.555************************************************************ PP

                           TIGR01123 151 tGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresll 225
                                         tG +k+gGnYaasl aq++a ++g+++vv+ld+ve++ +ee+G++n+f+  +dg+l t+pl++ iL+g+tr+sl+
  lcl|FitnessBrowser__Smeli:SMc02896 200 TGEAKCGGNYAASLAAQAEAMQEGCEQVVFLDAVERRFVEELGGMNVFFGFRDGSLQTPPLTGTILPGITRDSLI 274
                                         *************************************************************************** PP

                           TIGR01123 226 elakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkklrdeltdi 298
                                         +la+d+gl+v+e+  aid+++a +e+G +  +facGtaav+tP+g++k  ++++++ ++  G+v+ +l+ +l+di
  lcl|FitnessBrowser__Smeli:SMc02896 275 TLARDMGLTVREEPYAIDQWQADAESGRLteAFACGTAAVVTPIGKVKGREHSFTIGDGGAGPVASRLKSALLDI 349
                                         ***************************9999******************************************** PP

                           TIGR01123 299 qyGkledkegWiv 311
                                         q G++ d++gW+ 
  lcl|FitnessBrowser__Smeli:SMc02896 350 QNGRAPDPHGWLD 362
                                         ***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (365 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.87
//
[ok]

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

Links

Downloads

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:

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:

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:

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:

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