Alignments for a candidate for proB in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Desulfovibrio oxyclinae DSM 11498

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_018123773.1 B149_RS0103465 glutamate 5-kinase

Query= BRENDA::Q6E235
         (370 letters)



>NCBI__GCF_000375485.1:WP_018123773.1
          Length = 384

 Score =  242 bits (617), Expect = 1e-68
 Identities = 146/365 (40%), Positives = 214/365 (58%), Gaps = 13/365 (3%)

Query: 5   RIVVKIGSSSLTNSNGSIDEAKIKEHTEAISLLKENGHEVILITSGAVAAGFSAL----- 59
           R++VK+GS+ LT   G   EA I+   + +S L + G ++IL++SGAVAAG   +     
Sbjct: 16  RVLVKVGSAVLTREEGLNREAMIRLAGQ-LSRLHDRGMDIILVSSGAVAAGRKRMREAHN 74

Query: 60  GYPARPVTIKGKQAAAAVGQTLLMQQYMDHLKRYGLTPAQILLTRNDFSKRERYRNAYAT 119
           G       +  +QAA+AVGQ  LM  Y +    +G T AQIL+TR+  S R R+ NA  T
Sbjct: 75  GQMPDMDDLPARQAASAVGQGRLMHDYDEAFGWFGKTTAQILITRDGLSDRHRFLNARNT 134

Query: 120 VMELLERGVVPIINENDSTSVEELTFGDNDMLSALVSGLIHADQLMILTDINGLYDANPN 179
           +  LL  GV+PIINEND+ +V+EL FGDND L+A+  GL  AD  + LT  +G++D+NP+
Sbjct: 135 LERLLSWGVIPIINENDTVAVQELEFGDNDTLAAMALGLAGADLFVNLTSADGVFDSNPD 194

Query: 180 ENPDAKRFDYLTDITPELLGYAGSAGSKVGTGGMKSKFLAAQTALSLGVKVFIGTGAGRE 239
            NPDAK    + DI+           + VG+GGM SK  AA  A  LGV   I +G G  
Sbjct: 195 SNPDAKCLRIIEDISALDFETMCDGKTSVGSGGMYSKLRAAHRAAQLGVATLIVSGKGEF 254

Query: 240 KLKVILDGKGDGTYIGDKELSTVNNTRQWIMFHSPISGEIIIDGGAEQAMIHNGSSLLPA 299
            ++   + +  GT+I   E +TV++ + W+ +H   +G + +D GA +A+   G SLLPA
Sbjct: 255 SIEQAFEDERHGTFILPVE-NTVSSKKFWLAYHEDPAGTLTVDAGAARALTEGGKSLLPA 313

Query: 300 GVADVCGSFPKGAVVEVRGPGGIIGKGQTHYSSDEILEAKGKRSDQL-----PGAKQVEV 354
           G+  V G FP+G +V+V   G ++G G ++YSSDE+    GK S ++     P   Q E 
Sbjct: 314 GIKKVDGCFPRGTLVQVVADGDMLGVGLSNYSSDELHSIAGKNSSEIAQTIGPVPFQ-EA 372

Query: 355 IHRND 359
           IHR++
Sbjct: 373 IHRDN 377


Lambda     K      H
   0.314    0.134    0.377 

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: 394
Number of extensions: 21
Number of successful extensions: 5
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: 370
Length of database: 384
Length adjustment: 30
Effective length of query: 340
Effective length of database: 354
Effective search space:   120360
Effective search space used:   120360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_018123773.1 B149_RS0103465 (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.29398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-121  390.5   0.0   4.5e-121  390.3   0.0    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018123773.1  B149_RS0103465 glutamate 5-kinas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018123773.1  B149_RS0103465 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.3   0.0  4.5e-121  4.5e-121       2     362 ..      16     379 ..      15     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 390.3 bits;  conditional E-value: 4.5e-121
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglper.....pkkl 65 
                                               r+ vK+Gs++Lt+e+g l+r+ + +l+ q+++l++ G ++++vsSGavaaG +++   +        +l
  lcl|NCBI__GCF_000375485.1:WP_018123773.1  16 RVLVKVGSAVLTREEG-LNREAMIRLAGQLSRLHDRGMDIILVSSGAVAAGRKRMREAHNgqmpdMDDL 83 
                                               799************9.***********************************99976654111114689 PP

                                 TIGR01027  66 aekQalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDt 134
                                                 +Qa++aVGQgrLm+ y+++f ++g+++aQiL+tr+ ls+r+r+lNarntle+ll++gv+pi+NENDt
  lcl|NCBI__GCF_000375485.1:WP_018123773.1  84 PARQAASAVGQGRLMHDYDEAFGWFGKTTAQILITRDGLSDRHRFLNARNTLERLLSWGVIPIINENDT 152
                                               9******************************************************************** PP

                                 TIGR01027 135 vaveeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgs 203
                                               vav+e++fGDNDtL+a+   l +Adl v lt++dg++d++p +npdAk +  +e+i++   ++  ++ +
  lcl|NCBI__GCF_000375485.1:WP_018123773.1 153 VAVQELEFGDNDTLAAMALGLAGADLFVNLTSADGVFDSNPDSNPDAKCLRIIEDISALDFETMCDGKT 221
                                               ******************************************************************999 PP

                                 TIGR01027 204 svGTGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseak 272
                                               svG GGm +Kl aa+ A+++gv ++i+sg+ + +i ++ ed+  gt++ + +++++++k+w++++++++
  lcl|NCBI__GCF_000375485.1:WP_018123773.1 222 SVGSGGMYSKLRAAHRAAQLGVATLIVSGKGEFSIEQAFEDERHGTFILPVENTVSSKKFWLAYHEDPA 290
                                               ********************************************************************* PP

                                 TIGR01027 273 GkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkse 341
                                               G+++vd+ga++al+e gksLlpag+ +v g F rg  v+++a+ g ++g gl+nyss+el++i+g++s+
  lcl|NCBI__GCF_000375485.1:WP_018123773.1 291 GTLTVDAGAARALTEGGKSLLPAGIKKVDGCFPRGTLVQVVAD-GDMLGVGLSNYSSDELHSIAGKNSS 358
                                               ****************************************987.************************* PP

                                 TIGR01027 342 eiedvLgyekkeevvhrdnlv 362
                                               ei++ +g    +e++hrdnl+
  lcl|NCBI__GCF_000375485.1:WP_018123773.1 359 EIAQTIGPVPFQEAIHRDNLL 379
                                               *******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (384 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.80
//
[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