GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Phyllobacterium endophyticum PEPV15

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_106718540.1 CU100_RS21135 branched-chain amino acid aminotransferase

Query= reanno::BFirm:BPHYT_RS16285
         (307 letters)



>NCBI__GCF_003010935.1:WP_106718540.1
          Length = 296

 Score =  220 bits (561), Expect = 3e-62
 Identities = 115/262 (43%), Positives = 163/262 (62%), Gaps = 5/262 (1%)

Query: 7   DGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNS 66
           +G IWM+G+ + W DA+IHVLTH LHY   VFEG RAY     G  IF+L EHT+RL  S
Sbjct: 10  EGYIWMNGEFVRWTDARIHVLTHGLHYASSVFEGERAY-----GGEIFKLNEHTERLHES 64

Query: 67  AKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAAW 126
           A+I    +P+D E L  A  +++ +   +  Y+RPI W GSE +GVSA+ N I+VAIA W
Sbjct: 65  ARILGFKIPYDVEELNDACRKLLAKQGFQDAYVRPIAWRGSESMGVSAQANKINVAIAIW 124

Query: 127 PWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALL 186
            W +Y       +GIR+  + + R     +  ++KA+G Y+   ++   A A GY +AL+
Sbjct: 125 QWPSYFDPAQKLRGIRLDMAEYRRPDPRTAPSKSKAAGLYMICTISKHAAEAKGYADALM 184

Query: 187 LDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDE 246
           LD  G V+E +G N F V +G ++TP     LDGITR TVI LA+  G +V+E+ I  +E
Sbjct: 185 LDWRGQVAEATGANVFFVKDGIIHTPVPDCFLDGITRRTVIELAKRRGYEVVERVIMPEE 244

Query: 247 VYTCDEAFFTGTAAEVTPIREL 268
           +   ++ F TGTAAEVTP+ E+
Sbjct: 245 LVDFEQCFLTGTAAEVTPVSEI 266


Lambda     K      H
   0.319    0.136    0.411 

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: 251
Number of extensions: 8
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: 307
Length of database: 296
Length adjustment: 27
Effective length of query: 280
Effective length of database: 269
Effective search space:    75320
Effective search space used:    75320
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_106718540.1 CU100_RS21135 (branched-chain amino acid aminotransferase)
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.831191.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    5.1e-89  284.3   0.0    6.1e-89  284.1   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106718540.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106718540.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.1   0.0   6.1e-89   6.1e-89       1     281 [.      14     285 ..      14     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.1 bits;  conditional E-value: 6.1e-89
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w++Ge+v++ da++hvlth+lhY ++vfeG RaY +     if+l+eh+eRl++sa+il ++ipy  eel+++
  NCBI__GCF_003010935.1:WP_106718540.1  14 WMNGEFVRWTDARIHVLTHGLHYASSVFEGERAYGG----EIFKLNEHTERLHESARILGFKIPYDVEELNDA 82 
                                           9*********************************99....9******************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           ++++l k+++++aY+Rp++++G+e++g++++++ k++v+ia w+w+ y++     +Gi+  ++ +rr ++ + 
  NCBI__GCF_003010935.1:WP_106718540.1  83 CRKLLAKQGFQDAYVRPIAWRGSESMGVSAQAN-KINVAIAIWQWPSYFDPAQKLRGIRLDMAEYRRPDPRTA 154
                                           ******************************777.****************99999****************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p+k kaag Y+  ++ k+ a ++Gy +a++Ld  G vae +G n+f vkdg + tP   +  L+gitr +vi+
  NCBI__GCF_003010935.1:WP_106718540.1 155 PSKSKAAGLYMICTISKHAAEAKGYADALMLDWRGQVAEATGANVFFVKDGIIHTPVP-DCFLDGITRRTVIE 226
                                           ********************************************************99.99************ PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaff 281
                                           lak++g+ev+e++i  eel   +  fltGtaaevtP+ e+   +    ++G++  +l++ + 
  NCBI__GCF_003010935.1:WP_106718540.1 227 LAKRRGYEVVERVIMPEELVDFEQCFLTGTAAEVTPVSEISRYRF---TVGEIAINLMNDYA 285
                                           ****************************************98876...46777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (296 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: 25.82
//
[ok]

This GapMind analysis is from Jul 26 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