Alignments for a candidate for asp-kinase in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfacinum hydrothermale DSM 13146

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_084056507.1 B9A12_RS03940 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_900176285.1:WP_084056507.1
          Length = 417

 Score =  461 bits (1187), Expect = e-134
 Identities = 237/404 (58%), Positives = 311/404 (76%), Gaps = 2/404 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MAL+VQK+GGTSV  ++RI  VA++V + R+AGDDLVVVLSA +G+T+ L++LA Q++ Q
Sbjct: 1   MALVVQKYGGTSVADVDRIRNVAKRVIERRKAGDDLVVVLSARAGDTDHLLELAHQMSPQ 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P PRELDV+++TGEQVTIAL +MA+   G  AVS TG Q  I+TD  H  ARI  I+   
Sbjct: 61  PDPRELDVLLATGEQVTIALFSMAVKDLGFEAVSMTGYQAGIITDHHHGHARISWIETLP 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           ++  LKEG++VVVAGFQG D+ G+ITTLGRGGSDTT VALAA+LKAD C+IYTDV+GVYT
Sbjct: 121 VKEKLKEGKIVVVAGFQGYDDEGNITTLGRGGSDTTAVALAASLKADACEIYTDVEGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240
           TDP V  +AR+L KI++EEMLEMAS+G+KVL IRSVEF  KYNVP+ V  SF + PGTL+
Sbjct: 181 TDPNVYSKARKLRKISYEEMLEMASMGAKVLHIRSVEFGMKYNVPIWVRSSFTDDPGTLV 240

Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300
           T  E+  ME+ ++SG+ ++++EA++T+  VPD PG+AFKI  PI+ + I VDMI+Q  + 
Sbjct: 241 TA-EDPDMEKVVVSGVTYSKNEARVTVTDVPDLPGMAFKIFEPIAHAGINVDMIIQGSSG 299

Query: 301 -DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASC 359
                + +FTV + +YE+  ++ E   +EIGA  V G   IAK+S++GVGMRSH GVAS 
Sbjct: 300 VPGRANISFTVPKADYEQTLALAEKATKEIGAGPVHGTPHIAKISVIGVGMRSHTGVASL 359

Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDL 403
           MF+ LAKE+INI MISTSEIK+S V++EKY ELAVR LH AF+L
Sbjct: 360 MFDCLAKENINIHMISTSEIKISCVIDEKYTELAVRVLHDAFEL 403


Lambda     K      H
   0.316    0.133    0.358 

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: 531
Number of extensions: 18
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: 411
Length of database: 417
Length adjustment: 31
Effective length of query: 380
Effective length of database: 386
Effective search space:   146680
Effective search space used:   146680
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_084056507.1 B9A12_RS03940 (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.22799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-141  457.7   2.6   2.2e-141  457.5   2.6    1.0  1  lcl|NCBI__GCF_900176285.1:WP_084056507.1  B9A12_RS03940 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084056507.1  B9A12_RS03940 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.5   2.6  2.2e-141  2.2e-141       1     406 [.       1     403 [.       1     404 [. 0.98

  Alignments for each domain:
  == domain 1  score: 457.5 bits;  conditional E-value: 2.2e-141
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + l+VqK+GGtsv++++ri+++ak+v+++ k g++ vVV+SA ++ td+l+ela      +++s ++ p
  lcl|NCBI__GCF_900176285.1:WP_084056507.1   1 MALVVQKYGGTSVADVDRIRNVAKRVIERRKAGDDLVVVLSARAGDTDHLLELA------HQMSPQPDP 63 
                                               579***************************************************......8******** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d l+++GE++++al+s+a+++lg +a++++g +agi+Td ++g+A+i+ ++t   + e L+eg+iv
  lcl|NCBI__GCF_900176285.1:WP_084056507.1  64 RELDVLLATGEQVTIALFSMAVKDLGFEAVSMTGYQAGIITDHHHGHARISWIET-LPVKEKLKEGKIV 131
                                               *******************************************************.************* PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               vvaGF+G + eG+iTtLGRGGSD+tA++laa+lkAd +eiyTDVeGvyttDP+v ++a+k+ kisyeE+
  lcl|NCBI__GCF_900176285.1:WP_084056507.1 132 VVAGFQGYDDEGNITTLGRGGSDTTAVALAASLKADACEIYTDVEGVYTTDPNVYSKARKLRKISYEEM 200
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltveg 273
                                               le+A++Gakvlh r++e+ ++++vpi vrss+  + gTl+t+   ++e+  +v++++++kn ar+tv+ 
  lcl|NCBI__GCF_900176285.1:WP_084056507.1 201 LEMASMGAKVLHIRSVEFGMKYNVPIWVRSSFTDDPGTLVTAedpDMEKV-VVSGVTYSKNEARVTVT- 267
                                               *****************************************987667766.*****************. PP

                                 TIGR00656 274 egmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesle 338
                                                ++ + +g++ +if+ +a+++invd+i+q++s      +is++v + d +++ ++ ++ +++++   ++
  lcl|NCBI__GCF_900176285.1:WP_084056507.1 268 -DVPDLPGMAFKIFEPIAHAGINVDMIIQGSSGvpgrANISFTVPKADYEQTLALAEKATKEIGAGPVH 335
                                               .*****************************98777779******************************* PP

                                 TIGR00656 339 veedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                                   +a++s++g+g+++++Gvas +f  l+++nini mis+se+kis ++dek++e avr lh+++e+
  lcl|NCBI__GCF_900176285.1:WP_084056507.1 336 GTPHIAKISVIGVGMRSHTGVASLMFDCLAKENINIHMISTSEIKISCVIDEKYTELAVRVLHDAFEL 403
                                               *****************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (417 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.09
//
[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