GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Caulobacter crescentus NA1000

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate CCNA_03024 CCNA_03024 branched-chain amino acid aminotransferase

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



>FitnessBrowser__Caulo:CCNA_03024
          Length = 296

 Score =  243 bits (621), Expect = 3e-69
 Identities = 123/264 (46%), Positives = 167/264 (63%), Gaps = 5/264 (1%)

Query: 5   DRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLL 64
           DRDG IW+DG+ + WR+AK+HVLTH LHY   VFEG R Y     G  IF+L EHT+RL 
Sbjct: 8   DRDGWIWLDGQFVPWREAKVHVLTHGLHYASSVFEGERMY-----GGEIFKLTEHTERLF 62

Query: 65  NSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIA 124
            SA+I   ++P+    +  A      +N L+ CY+RPI W GSE +GVSA+ + IHVAIA
Sbjct: 63  KSAEILDFEIPYTVAEIDEACKATAAKNGLKDCYVRPIAWRGSEMIGVSAQQSKIHVAIA 122

Query: 125 AWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEA 184
            W W +Y      AKGIR+  + + R     + + AKA+G Y+   ++   A  DGY +A
Sbjct: 123 VWEWPSYFDPATKAKGIRLTWAKYQRPDPKTAPIAAKAAGLYMICTISKHAAEKDGYADA 182

Query: 185 LLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITR 244
           ++LD  GYV+E +G N F V +G L+TP     LDGITR TVI LA+  GI+V+E+ I +
Sbjct: 183 MMLDYRGYVAEATGANVFFVKDGVLHTPKPDCFLDGITRRTVIDLAKAKGIEVVERHIQK 242

Query: 245 DEVYTCDEAFFTGTAAEVTPIREL 268
           +E+ T  E F  GTAAEVTP+ E+
Sbjct: 243 EELATFTECFIVGTAAEVTPVSEV 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: 304
Number of extensions: 11
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 CCNA_03024 CCNA_03024 (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.2981168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-92  295.1   0.0    2.9e-92  295.0   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03024  CCNA_03024 branched-chain amino 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03024  CCNA_03024 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.0   0.0   2.9e-92   2.9e-92       1     287 [.      14     291 ..      14     296 .] 0.96

  Alignments for each domain:
  == domain 1  score: 295.0 bits;  conditional E-value: 2.9e-92
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           wldG++v++++akvhvlth+lhY ++vfeG R+Y +     if+l+eh+eRl++sa+il++eipy+  e+ e+
  lcl|FitnessBrowser__Caulo:CCNA_03024  14 WLDGQFVPWREAKVHVLTHGLHYASSVFEGERMYGG----EIFKLTEHTERLFKSAEILDFEIPYTVAEIDEA 82 
                                           9*********************************99....9******************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           +k +  kn+lk++Y+Rp++++G+e +g+++  + k++v+ia+wew+ y++  +  kGi+ + + ++r ++++ 
  lcl|FitnessBrowser__Caulo:CCNA_03024  83 CKATAAKNGLKDCYVRPIAWRGSEMIGVSA-QQSKIHVAIAVWEWPSYFDPATKAKGIRLTWAKYQRPDPKTA 154
                                           ******************************.778*************************************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p +akaag Y+  ++ k+ a + Gy +a++Ld  Gyvae +G n+f vkdgvl tP+  +  L+gitr +vi+
  lcl|FitnessBrowser__Caulo:CCNA_03024 155 PIAAKAAGLYMICTISKHAAEKDGYADAMMLDYRGYVAEATGANVFFVKDGVLHTPKP-DCFLDGITRRTVID 226
                                           *********************************************************9.99************ PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287
                                           lak +giev+e++i +eel t  e f+ GtaaevtP+ ev + k    k   +   l++++  lv+g+
  lcl|FitnessBrowser__Caulo:CCNA_03024 227 LAKAKGIEVVERHIQKEELATFTECFIVGTAAEVTPVSEVGEFKFTPAK---LSLDLMDTYAALVRGE 291
                                           ****************************************999987654...5667777777777776 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: 15.27
//
[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:

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