Alignments for a candidate for ilvE in Sinorhizobium meliloti 1021

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.7101.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.89
//
[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