Alignments for a candidate for ilvE in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Persephonella marina EX-H1

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_015898939.1 PERMA_RS06100 branched-chain amino acid transaminase

Query= BRENDA::F0QW25
         (314 letters)



>NCBI__GCF_000021565.1:WP_015898939.1
          Length = 302

 Score =  305 bits (780), Expect = 1e-87
 Identities = 142/301 (47%), Positives = 215/301 (71%), Gaps = 1/301 (0%)

Query: 14  MKYVWVNGKLIPEKEATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHD 73
           M+Y++  GK++PE +A I I T++ HYGT+IFEGIRAY++ D + ++    ++HY R   
Sbjct: 1   MEYIYFEGKIVPEDQAKISIKTNSFHYGTAIFEGIRAYYDKDTDRMWGLFFKEHYERLFQ 60

Query: 74  SAKIMSIKVGYSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAII 133
           + K++++++  S+D+L++ T EL+R N++ +D+YIRPI + S   ++  +       AI 
Sbjct: 61  NMKVLNMEIEESIDQLVEITKELIRKNNIKDDIYIRPIVYFSDLKISPKLVGYKSRIAIY 120

Query: 134 TVPFGHYLE-PKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILL 192
           T P G Y++  KGIKA V SW R++++M P + KV+G YVNS  +  +A ++G DEAI+L
Sbjct: 121 TYPLGDYIDINKGIKAIVSSWTRINDNMIPPRLKVAGSYVNSAFSKTEAILAGADEAIVL 180

Query: 193 NRDGYVAEGSGENIFIIKDGILYTPPVYDSILEGITRDTVITIARDLGLTVTEKRITREE 252
           N++GYV+EGS ENIFI++DG L TPPV D ILEGITR+ +ITIA+DLG  V E+ I+R E
Sbjct: 181 NKNGYVSEGSAENIFIVRDGKLITPPVSDDILEGITRNAIITIAKDLGYQVIERHISRTE 240

Query: 253 LYTADEVFFTGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVHGRVSKYKNWLTP 312
           LY ADE+FF GT A+V+PVV +D R IG+G PG I  +++  Y + V G++ KY++W+ P
Sbjct: 241 LYIADEIFFCGTGAQVSPVVEVDHRKIGDGSPGKITKEIQEVYFNAVRGKIEKYRHWVIP 300

Query: 313 I 313
           I
Sbjct: 301 I 301


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: 331
Number of extensions: 13
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: 314
Length of database: 302
Length adjustment: 27
Effective length of query: 287
Effective length of database: 275
Effective search space:    78925
Effective search space used:    78925
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_015898939.1 PERMA_RS06100 (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.25084.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-117  378.0   1.1   1.7e-117  377.8   1.1    1.0  1  lcl|NCBI__GCF_000021565.1:WP_015898939.1  PERMA_RS06100 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_015898939.1  PERMA_RS06100 branched-chain amino acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.8   1.1  1.7e-117  1.7e-117       1     296 [.       5     299 ..       5     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 377.8 bits;  conditional E-value: 1.7e-117
                                 TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglai..frlkehveRlydsakilrleipysk 67 
                                               +++G++v++++ak+++ t+++hYGt++feGiRaY  ++  ++  +++keh+eRl+++ k+l++ei+ s 
  lcl|NCBI__GCF_000021565.1:WP_015898939.1   5 YFEGKIVPEDQAKISIKTNSFHYGTAIFEGIRAYYDKDTDRMwgLFFKEHYERLFQNMKVLNMEIEESI 73 
                                               89*******************************98777555423789********************** PP

                                 TIGR01122  68 eelvevtkevlrknnlks.aYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvk 134
                                               ++lve+tke++rknn+k+  YiRp+vy  + dl+++pk v++k +++i+++++g y++   ++kGik++
  lcl|NCBI__GCF_000021565.1:WP_015898939.1  74 DQLVEITKELIRKNNIKDdIYIRPIVY--FSDLKISPKlVGYKSRIAIYTYPLGDYID---INKGIKAI 137
                                               *****************99********..99***************************...79****** PP

                                 TIGR01122 135 vssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPp 203
                                               vss++r ++n+ip+++k+ag+Y+ns++ k+ea+ aG+deai+L+++Gyv+eGs enifiv+dg+l+tPp
  lcl|NCBI__GCF_000021565.1:WP_015898939.1 138 VSSWTRINDNMIPPRLKVAGSYVNSAFSKTEAILAGADEAIVLNKNGYVSEGSAENIFIVRDGKLITPP 206
                                               ********************************************************************* PP

                                 TIGR01122 204 vsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpv 272
                                               vs+ iL+gitr+a+i++ak+lg++v e++isr+ely+aDe+f+ Gt a v P++evD+rkig+g+ G++
  lcl|NCBI__GCF_000021565.1:WP_015898939.1 207 VSDDILEGITRNAIITIAKDLGYQVIERHISRTELYIADEIFFCGTGAQVSPVVEVDHRKIGDGSPGKI 275
                                               ********************************************************************* PP

                                 TIGR01122 273 tkklqeaffdlvegktekkeewlt 296
                                               tk++qe +f+ v+gk+ek+ +w+ 
  lcl|NCBI__GCF_000021565.1:WP_015898939.1 276 TKEIQEVYFNAVRGKIEKYRHWVI 299
                                               **********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (302 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.78
//
[ok]

This GapMind analysis is from Apr 10 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis