Alignments for a candidate for asp-kinase in Geobacter uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Geobacter uraniireducens Rf4

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011939191.1 GURA_RS11775 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_000016745.1:WP_011939191.1
          Length = 407

 Score =  495 bits (1274), Expect = e-144
 Identities = 254/408 (62%), Positives = 328/408 (80%), Gaps = 2/408 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MAL+VQK+GGTS+G+VERI  VA++V K  +AG+D+VVVVSAMSGETN+L+ LAN I E 
Sbjct: 1   MALVVQKYGGTSMGSVERIRNVAKRVAKTYDAGNDMVVVVSAMSGETNKLVALANDICEF 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
           P  RE DV+V++GEQV+IALL++ L   G  A SY G Q+ I+TD+A++KARI  IDDT 
Sbjct: 61  PDNREYDVLVASGEQVSIALLAICLKSMGYKAKSYHGWQIPIITDNAYSKARIESIDDTK 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           IRAD+K G ++VVAGFQGVD +GNITTLGRGGSDT+ VA+AAALKAD C+I+TDVDGVYT
Sbjct: 121 IRADIKDGTILVVAGFQGVDKDGNITTLGRGGSDTSAVAMAAALKADVCEIFTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240
           TDP +   A++++KI+++EMLE+ASLG+KVLQIR+VEFA KY+V + V  SF + PGT++
Sbjct: 181 TDPNICEDAKKIEKISYDEMLELASLGAKVLQIRSVEFAKKYDVDVHVRSSFNDNPGTMV 240

Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300
           T +D++  ME  ++SGIA++++E K+ +  VPD PG+A KIL P+S AN+ VDMIVQNV+
Sbjct: 241 TKEDKD--MEAVLVSGIAYDKNETKIAVMQVPDKPGIAAKILSPLSDANISVDMIVQNVS 298

Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360
               TDFTFTV + D+  AL I K+ A +I A+E + D NI+KVS+VGVGMRSHAGVA++
Sbjct: 299 EAGFTDFTFTVTKADFKKALAITKEVARDIDAKEVLTDENISKVSVVGVGMRSHAGVATK 358

Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408
           MF+ALAKE INIQMISTSEIKVSVV++ KY ELAVR LH AF L   A
Sbjct: 359 MFQALAKEGINIQMISTSEIKVSVVVDAKYTELAVRVLHDAFGLSGKA 406


Lambda     K      H
   0.317    0.133    0.362 

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: 453
Number of extensions: 10
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: 412
Length of database: 407
Length adjustment: 31
Effective length of query: 381
Effective length of database: 376
Effective search space:   143256
Effective search space used:   143256
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_011939191.1 GURA_RS11775 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (EC 2.7.2.4))

# 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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.16081.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-138  447.4  15.6   2.7e-138  447.3  15.6    1.0  1  lcl|NCBI__GCF_000016745.1:WP_011939191.1  GURA_RS11775 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016745.1:WP_011939191.1  GURA_RS11775 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.3  15.6  2.7e-138  2.7e-138       1     406 [.       1     402 [.       1     403 [. 0.98

  Alignments for each domain:
  == domain 1  score: 447.3 bits;  conditional E-value: 2.7e-138
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + l+VqK+GGts+gs+eri+++ak+v k++  g+++vVVvSAms++t++lv+la      + i + + +
  lcl|NCBI__GCF_000016745.1:WP_011939191.1   1 MALVVQKYGGTSMGSVERIRNVAKRVAKTYDAGNDMVVVVSAMSGETNKLVALA------NDICEFPDN 63 
                                               579***************************************************......89999**** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d lv+ GE++s+all+  l+  g+ka++++g++ +i+Td+ + +A+i++++   ++   +++g+i 
  lcl|NCBI__GCF_000016745.1:WP_011939191.1  64 REYDVLVASGEQVSIALLAICLKSMGYKAKSYHGWQIPIITDNAYSKARIESIDD-TKIRADIKDGTIL 131
                                               ******************************************************9.9************ PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               vvaGF+G +++G+iTtLGRGGSD++A+++aaalkAd +ei+TDV+GvyttDP++ e+akki+kisy+E+
  lcl|NCBI__GCF_000016745.1:WP_011939191.1 132 VVAGFQGVDKDGNITTLGRGGSDTSAVAMAAALKADVCEIFTDVDGVYTTDPNICEDAKKIEKISYDEM 200
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273
                                               lelA+lGakvl+ r++e+a++++v + vrss++ + gT +t+   ++e   lv++ia++kn ++++v+ 
  lcl|NCBI__GCF_000016745.1:WP_011939191.1 201 LELASLGAKVLQIRSVEFAKKYDVDVHVRSSFNDNPGTMVTKedkDMEA-VLVSGIAYDKNETKIAVM- 267
                                               *****************************************97433444.6*****************. PP

                                 TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslev 339
                                                ++ +k+gi+a+i + L++++i+vd+i+q  se   t+ +++v + d ++a ++ ke+  +++ +++ +
  lcl|NCBI__GCF_000016745.1:WP_011939191.1 268 -QVPDKPGIAAKILSPLSDANISVDMIVQNVSEagfTDFTFTVTKADFKKALAITKEVARDIDAKEVLT 335
                                               .********************************99********************************** PP

                                 TIGR00656 340 eedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                               +e++ +vs+vg+g++++ Gva+++f+al++++ini mis+se+k+sv+vd k++e avr lh+++ +
  lcl|NCBI__GCF_000016745.1:WP_011939191.1 336 DENISKVSVVGVGMRSHAGVATKMFQALAKEGINIQMISTSEIKVSVVVDAKYTELAVRVLHDAFGL 402
                                               ***************************************************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (407 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.28
//
[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