Alignments for a candidate for asp-kinase in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Hydrogenovibrio halophilus DSM 15072

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_019895954.1 A377_RS0108830 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000384235.1:WP_019895954.1
          Length = 408

 Score =  518 bits (1335), Expect = e-152
 Identities = 266/407 (65%), Positives = 336/407 (82%), Gaps = 3/407 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MALIVQK+GGTSVGSIERI++VAEKV++   +GD +VV +SAMSGETNRL  +A++I   
Sbjct: 1   MALIVQKYGGTSVGSIERIQKVAEKVRRAVSSGDQVVVTVSAMSGETNRLTAMAQEIQSS 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P  RE+DV+++TGEQVTIALL MAL  +G PAVSYTG QV I T+  H KARI  I+  K
Sbjct: 61  PNRREMDVLLTTGEQVTIALLAMALESQGQPAVSYTGWQVPIHTNDVHAKARIESIEADK 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           I   L +G+VVV+AGFQGV + G I+TLGRGGSDTT VALAAAL ADECQIYTDVDGVYT
Sbjct: 121 IHWQLGQGKVVVIAGFQGVTDQGDISTLGRGGSDTTAVALAAALNADECQIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240
           TDPRVVP+ARRLE IT++EMLE+ASLG+KVLQIRSVEFA KY+VPLRVL S +EG GTL+
Sbjct: 181 TDPRVVPEARRLETITYDEMLELASLGAKVLQIRSVEFASKYHVPLRVLSSMQEGGGTLL 240

Query: 241 TID---EEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQN 297
             +   EE +ME+P+ISGIAF+RDEAKL + GVPD PG+A+++LGP+S +NIE+DMI+QN
Sbjct: 241 ISEEEFEERAMEKPLISGIAFSRDEAKLMVLGVPDEPGIAYQLLGPVSDANIEIDMIIQN 300

Query: 298 VAHDNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVA 357
            + D TTDFTFTV RN+  +A++++E TA+ + AR+V+ D  IAK+S+VG+GM+SH+G+A
Sbjct: 301 QSVDGTTDFTFTVTRNDLAQAKALMEATAKRLNARQVLSDDSIAKLSMVGIGMKSHSGIA 360

Query: 358 SCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           S MF+ LA   INIQMI T+EIK+SVV++E  L+ AVRALH+AF+LD
Sbjct: 361 STMFKTLADHEINIQMIGTTEIKISVVIDEGRLDEAVRALHSAFELD 407


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: 479
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: 411
Length of database: 408
Length adjustment: 31
Effective length of query: 380
Effective length of database: 377
Effective search space:   143260
Effective search space used:   143260
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_019895954.1 A377_RS0108830 (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.5479.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-132  428.5  10.6   1.5e-132  428.4  10.6    1.0  1  lcl|NCBI__GCF_000384235.1:WP_019895954.1  A377_RS0108830 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384235.1:WP_019895954.1  A377_RS0108830 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.4  10.6  1.5e-132  1.5e-132       1     406 [.       1     406 [.       1     407 [. 0.98

  Alignments for each domain:
  == domain 1  score: 428.4 bits;  conditional E-value: 1.5e-132
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liVqK+GGtsvgs+eri+k+a++v +++++g++vvV vSAms++t++l ++a      + i++ +++
  lcl|NCBI__GCF_000384235.1:WP_019895954.1   1 MALIVQKYGGTSVGSIERIQKVAEKVRRAVSSGDQVVVTVSAMSGETNRLTAMA------QEIQSSPNR 63 
                                               579***************************************************......799****** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re+d l+ +GE++++all++al+ +g+ a++++g++ +i T+d + +A+i++++   ++  +L +g++v
  lcl|NCBI__GCF_000384235.1:WP_019895954.1  64 REMDVLLTTGEQVTIALLAMALESQGQPAVSYTGWQVPIHTNDVHAKARIESIEA-DKIHWQLGQGKVV 131
                                               *******************************************************.9************ PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               v+aGF+G t +G+i tLGRGGSD+tA++laaal+Ad+++iyTDV+GvyttDPrvv+ea+++++i+y+E+
  lcl|NCBI__GCF_000384235.1:WP_019895954.1 132 VIAGFQGVTDQGDISTLGRGGSDTTAVALAAALNADECQIYTDVDGVYTTDPRVVPEARRLETITYDEM 200
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.......kkensslvkaialeknvarl 269
                                               lelA+lGakvl+ r++e+a +++vp++v ss ++  gTl+++        +e++ l+++ia++++ a+l
  lcl|NCBI__GCF_000384235.1:WP_019895954.1 201 LELASLGAKVLQIRSVEFASKYHVPLRVLSSMQEGGGTLLISeeefeerAMEKP-LISGIAFSRDEAKL 268
                                               ***************************************999888887666666.************** PP

                                 TIGR00656 270 tvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaele 335
                                                v   g+ +++gi+ ++ + +++++i +d+i+q +s    t+ +++v ++d+ +ak++++++ + ++ +
  lcl|NCBI__GCF_000384235.1:WP_019895954.1 269 MVL--GVPDEPGIAYQLLGPVSDANIEIDMIIQNQSVdgtTDFTFTVTRNDLAQAKALMEATAKRLNAR 335
                                               ***..9*****************************97888***************************** PP

                                 TIGR00656 336 sleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404
                                               ++  +  +a++s+vg g+++++G+as +fk l++++ini mi++ e+kisv++de  + +avr+lh+++
  lcl|NCBI__GCF_000384235.1:WP_019895954.1 336 QVLSDDSIAKLSMVGIGMKSHSGIASTMFKTLADHEINIQMIGTTEIKISVVIDEGRLDEAVRALHSAF 404
                                               ********************************************************************* PP

                                 TIGR00656 405 ee 406
                                               e+
  lcl|NCBI__GCF_000384235.1:WP_019895954.1 405 EL 406
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (408 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: 00:00:00.01
# Mc/sec: 10.09
//
[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