GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Thermocrinis albus DSM 14484

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_041434172.1 THAL_RS02350 branched-chain-amino-acid transaminase

Query= BRENDA::F0QW25
         (314 letters)



>NCBI__GCF_000025605.1:WP_041434172.1
          Length = 305

 Score =  305 bits (780), Expect = 1e-87
 Identities = 149/303 (49%), Positives = 211/303 (69%), Gaps = 2/303 (0%)

Query: 14  MKYVWVNGKLIPEKEATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHD 73
           M+Y +  G+++P +EA I I T++ HYGT++FEGIRAYWN +++ LY+  AR+HY R   
Sbjct: 1   MEYAFFEGRIVPIEEAKISIKTNSFHYGTAVFEGIRAYWNEEHHQLYILFAREHYQRLLA 60

Query: 74  SAKIMSIKVGYSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAII 133
           + + M +++ YSVD+L++ TVELLR N++  DVYIRPI +     +   +       AI 
Sbjct: 61  NCRAMFMELPYSVDDLVNITVELLRKNNIKHDVYIRPIAYFKDLALTPKLIGFTPEIAIY 120

Query: 134 TVPFGHYLE-PKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILL 192
           T  FG YL+  KGI+ K  SW+R  ++  P + KV+G YVNS +A  +A ++G+DEAI+L
Sbjct: 121 TYSFGRYLDTSKGIRVKTSSWIRNDDNSIPSRWKVAGAYVNSALAKTEAILAGYDEAIML 180

Query: 193 NRDGYVAEGSGENIFIIKDGILYTPPVYDSILEGITRDTVI-TIARDLGLTVTEKRITRE 251
           N++G+VAEGSGENIF+++   + TPP +D ILEGITR  VI  I  +L L V E+ I+R 
Sbjct: 181 NQNGFVAEGSGENIFLVRGRKVVTPPCWDHILEGITRSAVIKLIKNELVLEVEERSISRS 240

Query: 252 ELYTADEVFFTGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVHGRVSKYKNWLT 311
           ELY+ADEVF TGTAAE+TPVV ID R IG+G+ GPI  +++  Y D V G + +YK WLT
Sbjct: 241 ELYSADEVFLTGTAAEITPVVEIDNRKIGSGDIGPITRELQKIYFDAVRGNIERYKGWLT 300

Query: 312 PIY 314
           P+Y
Sbjct: 301 PVY 303


Lambda     K      H
   0.321    0.139    0.409 

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: 328
Number of extensions: 21
Number of successful extensions: 3
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: 314
Length of database: 305
Length adjustment: 27
Effective length of query: 287
Effective length of database: 278
Effective search space:    79786
Effective search space used:    79786
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: 48 (23.1 bits)

Align candidate WP_041434172.1 THAL_RS02350 (branched-chain-amino-acid transaminase)
to HMM TIGR01122 (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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.2594002.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-125  403.3   0.1   3.5e-125  403.1   0.1    1.0  1  NCBI__GCF_000025605.1:WP_041434172.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025605.1:WP_041434172.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.1   0.1  3.5e-125  3.5e-125       1     298 []       5     302 ..       5     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 403.1 bits;  conditional E-value: 3.5e-125
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk..glaifrlkehveRlydsakilrleipyskeelv 71 
                                           +++G++v++e+ak+++ t+++hYGt+vfeGiRaY++++  +l+i++++eh++Rl+ + +++ +e+pys ++lv
  NCBI__GCF_000025605.1:WP_041434172.1   5 FFEGRIVPIEEAKISIKTNSFHYGTAVFEGIRAYWNEEhhQLYILFAREHYQRLLANCRAMFMELPYSVDDLV 77 
                                           79*********************************98866899****************************** PP

                             TIGR01122  72 evtkevlrknnlks.aYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvkvssfrraa 142
                                           ++t+e+lrknn+k+ +YiRp++y  ++dl l+pk ++ ++e++i+++++g+yl++   +kGi+vk+ss+ r++
  NCBI__GCF_000025605.1:WP_041434172.1  78 NITVELLRKNNIKHdVYIRPIAY--FKDLALTPKlIGFTPEIAIYTYSFGRYLDT---SKGIRVKTSSWIRND 145
                                           ************988********..9****************************7...7************** PP

                             TIGR01122 143 vnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrd 215
                                           +nsip+++k+ag+Y+ns+lak+ea+ aGydeai+L+++G+vaeGsGenif+v+  +++tPp  ++iL+gitr 
  NCBI__GCF_000025605.1:WP_041434172.1 146 DNSIPSRWKVAGAYVNSALAKTEAILAGYDEAIMLNQNGFVAEGSGENIFLVRGRKVVTPPCWDHILEGITRS 218
                                           ************************************************************************* PP

                             TIGR01122 216 aviklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287
                                           avikl+k el++ev+e++isr+ely aDevfltGtaae+tP++e+D+rkig+g +Gp+t++lq+ +fd v+g+
  NCBI__GCF_000025605.1:WP_041434172.1 219 AVIKLIKnELVLEVEERSISRSELYSADEVFLTGTAAEITPVVEIDNRKIGSGDIGPITRELQKIYFDAVRGN 291
                                           *****99789*************************************************************** PP

                             TIGR01122 288 tekkeewltyv 298
                                           +e++++wlt+v
  NCBI__GCF_000025605.1:WP_041434172.1 292 IERYKGWLTPV 302
                                           ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (305 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.33
//
[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