Alignments for a candidate for proB in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Xenophilus azovorans DSM 13620

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_038209670.1 Q392_RS15735 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_000745855.1:WP_038209670.1
          Length = 382

 Score =  291 bits (744), Expect = 3e-83
 Identities = 165/366 (45%), Positives = 224/366 (61%), Gaps = 1/366 (0%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           + D++ +VVK+G+S++T   R L+   I E  RQ A L  AG  +V+V+SGA+A G + L
Sbjct: 11  LRDARRIVVKVGSSLVTNEGRGLDERAIGEWCRQLAGLVKAGREVVMVSSGAVAEGMKRL 70

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           G+   P  I   Q  AAVGQ  L Q++E      G+   Q+LLT  D+ DRER+LNAR T
Sbjct: 71  GWTARPKEINELQAAAAVGQMGLAQMYETKLRENGLGSAQVLLTHGDLADRERYLNARST 130

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           L  LLD N+VPVINEND V   EIK GDND L AL A L  AD L++LTDQKGL+TADPR
Sbjct: 131 LLTLLDLNVVPVINENDTVVNDEIKFGDNDTLGALVANLVEADALVILTDQKGLFTADPR 190

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
           S+P A  +      D AL A+AG + S +G GGM TK+ AA  A  +G  T+IA G +P 
Sbjct: 191 SHPDASFVHVGQAGDPALEAMAGGAGSSIGRGGMLTKILAAKRAAGSGASTVIAWGREPD 250

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299
            +  +  G ++GTL  AQ    + RKRW+       G +TVD GA A +   G SLLP G
Sbjct: 251 ALLRLARGEAIGTLLVAQTAKHQARKRWMADHLQLRGAVTVDAGAAAKVRSEGKSLLPIG 310

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +  V G+FSRG+VI + + +G ++A G++ Y+S   R +    S E + +LGY   P  V
Sbjct: 311 MVGVEGDFSRGDVIAVRDPQGVELARGLANYSSAEARLLCRKPSGEFERLLGYAGEPEMV 370

Query: 360 HRDDMI 365
           HRD+++
Sbjct: 371 HRDNLV 376


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: 370
Number of extensions: 17
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: 367
Length of database: 382
Length adjustment: 30
Effective length of query: 337
Effective length of database: 352
Effective search space:   118624
Effective search space used:   118624
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 WP_038209670.1 Q392_RS15735 (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.3641990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-131  423.3   0.1     5e-131  423.1   0.1    1.0  1  NCBI__GCF_000745855.1:WP_038209670.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038209670.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.1   0.1    5e-131    5e-131       1     362 [.      15     376 ..      15     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: 423.1 bits;  conditional E-value: 5e-131
                             TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaa 73 
                                           +riVvK+Gss++t+e + l++  + e ++q+a l kaG+evv+vsSGava G+++Lg + rpk+++e Qa+aa
  NCBI__GCF_000745855.1:WP_038209670.1  15 RRIVVKVGSSLVTNEGRGLDERAIGEWCRQLAGLVKAGREVVMVSSGAVAEGMKRLGWTARPKEINELQAAAA 87 
                                           59*************999******************************************************* PP

                             TIGR01027  74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDND 146
                                           VGQ  L + ye+++ + gl +aQ+LLt+ dl++rerylNar+tl +ll+l+vvp++NENDtv  +eikfGDND
  NCBI__GCF_000745855.1:WP_038209670.1  88 VGQMGLAQMYETKLRENGLGSAQVLLTHGDLADRERYLNARSTLLTLLDLNVVPVINENDTVVNDEIKFGDND 160
                                           ************************************************************************* PP

                             TIGR01027 147 tLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaael 219
                                           tL alva+lveAd+Lv+ltd++gL++adpr++pdA ++++ ++ + +l+a+ag++gss+G GGm tK+ aa+ 
  NCBI__GCF_000745855.1:WP_038209670.1 161 TLGALVANLVEADALVILTDQKGLFTADPRSHPDASFVHVGQAGDPALEAMAGGAGSSIGRGGMLTKILAAKR 233
                                           ************************************************************************* PP

                             TIGR01027 220 AsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksL 292
                                           A+ +g  ++ia g++p+++++l++++a+gtl+ a+++k ++rk+w++ +++ +G+++vd+ga+++++++gksL
  NCBI__GCF_000745855.1:WP_038209670.1 234 AAGSGASTVIAWGREPDALLRLARGEAIGTLLVAQTAKHQARKRWMADHLQLRGAVTVDAGAAAKVRSEGKSL 306
                                           ************************************************************************* PP

                             TIGR01027 293 lpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                           lp g+v+veg+Fsrg+v+ +++++g e+++gl+nyss+e + +++++s e e +Lgy  + e vhrdnlv
  NCBI__GCF_000745855.1:WP_038209670.1 307 LPIGMVGVEGDFSRGDVIAVRDPQGVELARGLANYSSAEARLLCRKPSGEFERLLGYAGEPEMVHRDNLV 376
                                           ********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (382 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: 00:00:00.00
# Mc/sec: 18.72
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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