Alignments for a candidate for proB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Desulfovibrio vulgaris Hildenborough

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 206361 DVU0930 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>MicrobesOnline__882:206361
          Length = 380

 Score =  265 bits (678), Expect = 1e-75
 Identities = 156/369 (42%), Positives = 230/369 (62%), Gaps = 8/369 (2%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           + +++ +VVK+G++VLT  +  +N A I  L  Q + L  +G R+V+V+SGA+AAGR  L
Sbjct: 11  LREARCVVVKVGSAVLTTETG-VNLAVIDSLAAQLSALQESGKRVVLVSSGAVAAGRSAL 69

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
                 A +  KQ  +AVGQSRL+  +++ F+ YG    Q+LLTR D+ +RERFLNAR+T
Sbjct: 70  RDCCEIAGMPHKQAASAVGQSRLMHHYDEAFARYGHLSAQVLLTRDDLRNRERFLNARNT 129

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
            +ALLD  ++PV+NEND VA  E+K GDND L++L   +   D  + LT   G+Y  +P+
Sbjct: 130 FQALLDWGVIPVVNENDTVAVQELKFGDNDCLASLLLNVVEGDLYVNLTSASGVYADNPQ 189

Query: 181 SNPQAEL---IKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGS 237
           +NP+A +   I+DV+ +D  L  + G   S +GTGGM +KL AA  A + G+ T+I  G 
Sbjct: 190 TNPEAGILPCIEDVHTLD--LDVMCGGKTS-VGTGGMYSKLLAASRAAQLGVPTLILPGR 246

Query: 238 KPGVIGDVMEGISVGTLFHAQATPLENRKRWI-FGAPPAGEITVDEGATAAILERGSSLL 296
           +P ++     G  VGT    +A  +  RK W+ + + P+G +TVDEGA  A+L++G SLL
Sbjct: 247 EPRILERAFSGEPVGTWVRPEARVVSRRKYWLAYQSEPSGTVTVDEGAARALLQQGGSLL 306

Query: 297 PKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGP 356
           P G+  V+G F  G ++RI   +G  IA G+S Y    L RI GH   E+ AILG  + P
Sbjct: 307 PGGVCDVSGAFEPGALVRIAGPDGTVIAVGLSNYGDRDLVRIKGHRRHEVAAILGDAHFP 366

Query: 357 VAVHRDDMI 365
             VHRD+M+
Sbjct: 367 EVVHRDNML 375


Lambda     K      H
   0.318    0.135    0.384 

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: 375
Number of extensions: 23
Number of successful extensions: 4
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: 367
Length of database: 380
Length adjustment: 30
Effective length of query: 337
Effective length of database: 350
Effective search space:   117950
Effective search space used:   117950
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: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 206361 DVU0930 (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.1173.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     1e-123  399.0   0.0   1.2e-123  398.8   0.0    1.0  1  lcl|MicrobesOnline__882:206361  DVU0930 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206361  DVU0930 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.8   0.0  1.2e-123  1.2e-123       3     362 ..      17     375 ..      15     376 .. 0.99

  Alignments for each domain:
  == domain 1  score: 398.8 bits;  conditional E-value: 1.2e-123
                       TIGR01027   3 iVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgrLmk 81 
                                     +VvK+Gs++Lt+e+g ++++ + +l++q+++l++ G++vv+vsSGavaaG +aL      + + +kQa++aVGQ+rLm+
  lcl|MicrobesOnline__882:206361  17 VVVKVGSAVLTTETG-VNLAVIDSLAAQLSALQESGKRVVLVSSGAVAAGRSALRDCCEIAGMPHKQAASAVGQSRLMH 94 
                                     9***********999.*************************************************************** PP

                       TIGR01027  82 lyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalveAdl 160
                                     +y+++f++yg  +aQ+LLtr+dl++rer+lNarnt+++ll++gv+p+vNENDtvav+e+kfGDND L+ l+ ++ve dl
  lcl|MicrobesOnline__882:206361  95 HYDEAFARYGHLSAQVLLTRDDLRNRERFLNARNTFQALLDWGVIPVVNENDTVAVQELKFGDNDCLASLLLNVVEGDL 173
                                     ******************************************************************************* PP

                       TIGR01027 161 LvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasgekpekia 239
                                      v lt++ g+y ++p+tnp+A +++ +e++++    v  ++ +svGTGGm +Kl aa+ A+++gv+++i++g++p  + 
  lcl|MicrobesOnline__882:206361 174 YVNLTSASGVYADNPQTNPEAGILPCIEDVHTLDLDVMCGGKTSVGTGGMYSKLLAASRAAQLGVPTLILPGREPRILE 252
                                     ********************************999999999999*********************************** PP

                       TIGR01027 240 dlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegq 318
                                     ++ ++++vgt + ++++ ++ rk w++++se++G+++vdega++all++g sLlp gv +v+g F+ g  v+i  ++g+
  lcl|MicrobesOnline__882:206361 253 RAFSGEPVGTWVRPEARVVSRRKYWLAYQSEPSGTVTVDEGAARALLQQGGSLLPGGVCDVSGAFEPGALVRIAGPDGT 331
                                     ******************************************************************************* PP

                       TIGR01027 319 eigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                      i+ gl+ny   +l +ikg++ +e++++Lg  +  evvhrdn++
  lcl|MicrobesOnline__882:206361 332 VIAVGLSNYGDRDLVRIKGHRRHEVAAILGDAHFPEVVHRDNML 375
                                     ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (380 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: 12.20
//
[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