GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Herbaspirillum seropedicae SmR1

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS03330 HSERO_RS03330 branched-chain amino acid aminotransferase

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



>FitnessBrowser__HerbieS:HSERO_RS03330
          Length = 306

 Score =  521 bits (1341), Expect = e-152
 Identities = 247/307 (80%), Positives = 282/307 (91%), Gaps = 1/307 (0%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSMADRDGKIW DG+LIDWRDA +HVLTHTLHYGMGVFEGVRAYKT DG TAIFRLQEHT
Sbjct: 1   MSMADRDGKIWKDGELIDWRDATVHVLTHTLHYGMGVFEGVRAYKTPDG-TAIFRLQEHT 59

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           +RL NSAKIFQM+VP+DH+TLA AQ +VVREN+LESCY+RP+IW+GSEKLGVSAKGN IH
Sbjct: 60  RRLRNSAKIFQMEVPYDHDTLAQAQRQVVRENQLESCYIRPLIWIGSEKLGVSAKGNQIH 119

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           VA+AAW WGAYLGEDG+ KGIRVKTSSF+RHHVNVS+VRAKA G+Y+NSILANQEA+ADG
Sbjct: 120 VAVAAWSWGAYLGEDGLNKGIRVKTSSFSRHHVNVSLVRAKACGYYINSILANQEALADG 179

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEALLLD +GYVSEGSGEN F+V NGK+YTPDL+SCLDGITRD V+T+ARD GI+VIEK
Sbjct: 180 YDEALLLDTEGYVSEGSGENVFIVKNGKIYTPDLASCLDGITRDAVLTMARDLGIEVIEK 239

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDE+Y  DEAFFTGTAAE+TPIRELD R IGSGARGP+TEKLQ+ FFD+V G++ +Y
Sbjct: 240 RITRDEMYCADEAFFTGTAAEITPIRELDRRVIGSGARGPVTEKLQTLFFDVVAGRAPQY 299

Query: 301 ANWLTKI 307
            +WLT +
Sbjct: 300 KHWLTLV 306


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: 449
Number of extensions: 6
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: 306
Length adjustment: 27
Effective length of query: 280
Effective length of database: 279
Effective search space:    78120
Effective search space used:    78120
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 HSERO_RS03330 HSERO_RS03330 (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.13126.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.1e-139  449.8   0.0   2.3e-139  449.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS03330  HSERO_RS03330 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS03330  HSERO_RS03330 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.6   0.0  2.3e-139  2.3e-139       1     298 []      11     306 .]      11     306 .] 0.99

  Alignments for each domain:
  == domain 1  score: 449.6 bits;  conditional E-value: 2.3e-139
                                  TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyske 68 
                                                w dGel+d++da+vhvlth+lhYG+gvfeG+RaY+t++g+aifrl+eh+ Rl +saki+++e+py ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS03330  11 WKDGELIDWRDATVHVLTHTLHYGMGVFEGVRAYKTPDGTAIFRLQEHTRRLRNSAKIFQMEVPYDHD 78 
                                                89****************************************************************** PP

                                  TIGR01122  69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvs 136
                                                +l +++++v+r+n+l+s+YiRpl+++G+e+lg+++k + +++v++aaw+wgaylge++l+kGi+vk+s
  lcl|FitnessBrowser__HerbieS:HSERO_RS03330  79 TLAQAQRQVVRENQLESCYIRPLIWIGSEKLGVSAKGN-QIHVAVAAWSWGAYLGEDGLNKGIRVKTS 145
                                                ***********************************655.9**************************** PP

                                  TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpv 204
                                                sf r++vn+   +aka g Y+ns+la++eal+ Gydea+lLd+eGyv+eGsGen+fivk+g+++tP++
  lcl|FitnessBrowser__HerbieS:HSERO_RS03330 146 SFSRHHVNVSLVRAKACGYYINSILANQEALADGYDEALLLDTEGYVSEGSGENVFIVKNGKIYTPDL 213
                                                ******************************************************************** PP

                                  TIGR01122 205 sesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpv 272
                                                  s+L+gitrdav+++a++lgiev e+ri+r+e+y aDe+f+tGtaae+tPire+D r ig+g rGpv
  lcl|FitnessBrowser__HerbieS:HSERO_RS03330 214 -ASCLDGITRDAVLTMARDLGIEVIEKRITRDEMYCADEAFFTGTAAEITPIRELDRRVIGSGARGPV 280
                                                .78***************************************************************** PP

                                  TIGR01122 273 tkklqeaffdlvegktekkeewltyv 298
                                                t+klq+ ffd+v g+ +++++wlt v
  lcl|FitnessBrowser__HerbieS:HSERO_RS03330 281 TEKLQTLFFDVVAGRAPQYKHWLTLV 306
                                                ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (306 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.24
//
[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