GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azohydromonas australica DSM 1124

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028997153.1 H537_RS0105945 branched-chain amino acid aminotransferase

Query= BRENDA::A0A2Z4MEX9
         (357 letters)



>NCBI__GCF_000430725.1:WP_028997153.1
          Length = 353

 Score =  299 bits (765), Expect = 9e-86
 Identities = 150/344 (43%), Positives = 218/344 (63%), Gaps = 3/344 (0%)

Query: 9   RTEQKKEKPASDKLGFGVHFTDHMFTMDY-TEGKGWHDPQIVPYSPLTLDPAAMVFHYGQ 67
           R E+K++ PA+ + GFG   +DHM  M Y  +  GW+ P+I PY   +L+P A+V HYGQ
Sbjct: 8   RAERKEKLPAA-QFGFGEKVSDHMLVMTYDADAGGWNRPEIKPYQSFSLEPRALVLHYGQ 66

Query: 68  AVFEGLKAYRNQEGKVRLFRPDQNFKRMNRSLERMSMPLIDEEFMVEALKQLVAVDKEWI 127
           ++FEGLKA+R  +G + LFRP+QN +RMN S  +M+MP I E   ++AL +LV ++++W+
Sbjct: 67  SIFEGLKAFRRPDGHIALFRPEQNIRRMNASARKMAMPEIPEALFMDALLKLVDIERDWV 126

Query: 128 PTESGQSLYIRPFVIATEPCFGVRASHTYKLVIVLSPVGAYYAGGMKPVKIYVENNYVRA 187
           P E+G SLYIRP +  ++   GVRA+  Y L ++LSPV  Y+  G KP K+    +  R 
Sbjct: 127 PAEAGASLYIRPLMFGSDAVLGVRAASRYILCVMLSPVPPYFVPGGKPFKLLAREDCART 186

Query: 188 VRGGTGNAKVAGNYAGSLKAQVEAKEKGYEQVLWLDGVENKYIEEVGSMNVFFKVKGEVW 247
           V GGTG+AK A NY  SL     A+ +GY+ +LWLD  +++++EE G  NVF +    V 
Sbjct: 187 VAGGTGDAKTAANYGRSLVPLDAARREGYDNLLWLDSEQHRFVEEAGITNVFVQYADRVV 246

Query: 248 TPALNGSILEGITRDSTIQLLKDWGIPVVEKRISMEDLHTAYVNGELEEAFGTGTAAVIS 307
           TP L+G IL GITRDS I+LL+D G  V+E+   + DL     +G + E F TGTA V++
Sbjct: 247 TPPLSGRILPGITRDSVIRLLRDEGRTVLEQETDIGDLVRDIDDGRVHEIFLTGTATVVA 306

Query: 308 PVGDLNWNGHQMIINGEKTGELTTRLYDEMTGIQYGDREDKFGW 351
           PV ++ + G +  +     G L   LY ++T IQYG   D+ GW
Sbjct: 307 PVDEIGFRGRRHALQIRDDG-LALSLYRQLTQIQYGLAPDRHGW 349


Lambda     K      H
   0.317    0.136    0.406 

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: 294
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 357
Length of database: 353
Length adjustment: 29
Effective length of query: 328
Effective length of database: 324
Effective search space:   106272
Effective search space used:   106272
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: 49 (23.5 bits)

Align candidate WP_028997153.1 H537_RS0105945 (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.772866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-103  331.3   0.0   2.9e-103  331.1   0.0    1.0  1  NCBI__GCF_000430725.1:WP_028997153.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_028997153.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.1   0.0  2.9e-103  2.9e-103       1     311 [.      42     351 ..      42     353 .] 0.98

  Alignments for each domain:
  == domain 1  score: 331.1 bits;  conditional E-value: 2.9e-103
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W+++e++++++++l++ + vlhYgq +feGlka+R  dG+i lfRp++n++R++ sa+++++Pe++e+lf++a
  NCBI__GCF_000430725.1:WP_028997153.1  42 WNRPEIKPYQSFSLEPRALVLHYGQSIFEGLKAFRRPDGHIALFRPEQNIRRMNASARKMAMPEIPEALFMDA 114
                                           9************************************************************************ PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           l +lv +++dwvp a+++asLY+RP++++ +++lGv+aa++y+++v++sPv +Yf  g +p + +  ++++R+
  NCBI__GCF_000430725.1:WP_028997153.1 115 LLKLVDIERDWVP-AEAGASLYIRPLMFGSDAVLGVRAASRYILCVMLSPVPPYFVPGGKPFKLLAREDCART 186
                                           *************.667******************************************************** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           + +GtG +k++ nY  sl +   a+++g+d+ ++ld+ +++ +ee+G +n+f+ + d ++vt+pls+ iL+g+
  NCBI__GCF_000430725.1:WP_028997153.1 187 VAGGTGDAKTAANYGRSLVPLDAARREGYDNLLWLDSEQHRFVEEAGITNVFVQYAD-RVVTPPLSGRILPGI 258
                                           ********************************************************9.*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+s+++l +d g +v e+e +i +l +  + G +  +f++Gta v++Pv e+   g+ + ++  + G ++ +
  NCBI__GCF_000430725.1:WP_028997153.1 259 TRDSVIRLLRDEGRTVLEQETDIGDLVRDIDDGRVheIFLTGTATVVAPVDEIGFRGRRHALQIRDDG-LALS 330
                                           *********************************9999**********************999988665.89** PP

                             TIGR01123 291 lrdeltdiqyGkledkegWiv 311
                                           l+ +lt+iqyG + d++gW+ 
  NCBI__GCF_000430725.1:WP_028997153.1 331 LYRQLTQIQYGLAPDRHGWMR 351
                                           *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (353 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: 00:00:00.00
# Mc/sec: 15.57
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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