Alignments for a candidate for proB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate Echvi_2634 Echvi_2634 glutamate 5-kinase

Query= curated2:Q3IP73
         (284 letters)



>FitnessBrowser__Cola:Echvi_2634
          Length = 268

 Score =  152 bits (383), Expect = 1e-41
 Identities = 94/253 (37%), Positives = 144/253 (56%), Gaps = 10/253 (3%)

Query: 28  KRVVVKAGTNSLTDEESNLDDDKLDKLVDDIADLLERDKDVLLVSSGAVGAGI----GRV 83
           KR+V+K GTN +T+ ++ + +  L K+VD IA L ER    +LVSSG+V AG      +V
Sbjct: 14  KRIVIKVGTNVMTNRDNRIVNTVLRKMVDQIAILYERGIMSVLVSSGSVIAGKEVLGSKV 73

Query: 84  GYGSRTVEESQALSTVGQSHLMRRYTESFERYDRKVAQILLTQQDLENPERFTNFCNTVE 143
           G   + +   Q  S VGQ  +MR Y   F+ Y  + AQ+L T++D +  +   N  N  E
Sbjct: 74  GIKDKIIRR-QVFSAVGQPRMMRHYYNIFQDYGMRCAQVLATKRDFDPGKHRENMINCYE 132

Query: 144 TLLEWDIVPIINENDAVATQEIRIGDNDMLSSSVAVGVDADLLVTLTDVDAVYTGNPKED 203
            LL   I+PI NE+DAV+       DND L+S VA    AD+L+ LTD D +Y G+P +D
Sbjct: 133 GLLSEGIIPIANEDDAVSLSMSTFTDNDELASLVAELTKADMLILLTDTDGLYNGHP-DD 191

Query: 204 PDAERIEAVGENYDQIQGLVEESSSSDF---GGIRTKVEGARNVSEYGIPAIIAGSAEPD 260
            + ERI  VG + ++++  ++ES+  +    GG+++K+  A+  +   IP  IA     +
Sbjct: 192 ENTERIAHVGTD-EKVEHFIQESTKGEAEGRGGMKSKLNVAKEAARKNIPTYIANGNVDN 250

Query: 261 VLQQIATGKSVGT 273
           ++  I  GK VGT
Sbjct: 251 MILDIVDGKEVGT 263


Lambda     K      H
   0.310    0.130    0.351 

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: 170
Number of extensions: 7
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: 284
Length of database: 268
Length adjustment: 25
Effective length of query: 259
Effective length of database: 243
Effective search space:    62937
Effective search space used:    62937
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate Echvi_2634 Echvi_2634 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.29806.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
      4e-68  216.1   0.9    4.5e-68  216.0   0.9    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2634  Echvi_2634 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2634  Echvi_2634 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   0.9   4.5e-68   4.5e-68       1     252 [.      14     266 ..      14     268 .] 0.96

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 4.5e-68
                            TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglper.pkklaekQalaa 73 
                                          kriV+K+G++++t+ ++++ ++ l+++v q+a l + G   v+vsSG+v aG e Lg +     k+  +Q+ +a
  lcl|FitnessBrowser__Cola:Echvi_2634  14 KRIVIKVGTNVMTNRDNRIVNTVLRKMVDQIAILYERGIMSVLVSSGSVIAGKEVLGSKVGiKDKIIRRQVFSA 87 
                                          69*******************************************************9976156799******* PP

                            TIGR01027  74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDt 147
                                          VGQ r+m++y ++f+ yg++ aQ+L t++d+   ++ +N  n  e ll+ g++pi NE D+v+ +  +f DND+
  lcl|FitnessBrowser__Cola:Echvi_2634  88 VGQPRMMRHYYNIFQDYGMRCAQVLATKRDFDPGKHRENMINCYEGLLSEGIIPIANEDDAVSLSMSTFTDNDE 161
                                          ************************************************************************** PP

                            TIGR01027 148 LsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagss.gssvGTGGmrtKleaaelA 220
                                          L+ lva l +Ad+L+lltd dgLy+  p  + + ++i +v   e+  + ++ s+ g++ G GGm++Kl+ a+ A
  lcl|FitnessBrowser__Cola:Echvi_2634 162 LASLVAELTKADMLILLTDTDGLYNGHP-DDENTERIAHVGTDEKVEHFIQESTkGEAEGRGGMKSKLNVAKEA 234
                                          ****************************.888999*****999998888887776888**************** PP

                            TIGR01027 221 sragveviiasgekpekiadlledaavgtlfe 252
                                          +r +++++ia+g+  + i+d++++++vgt++ 
  lcl|FitnessBrowser__Cola:Echvi_2634 235 ARKNIPTYIANGNVDNMILDIVDGKEVGTKVS 266
                                          *****************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (268 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: 10.43
//
[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:

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