Alignments for a candidate for asp-kinase in Sulfuritalea hydrogenivorans DSM 22779

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Sulfuritalea hydrogenivorans DSM 22779

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_041099485.1 SUTH_RS11835 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000828635.1:WP_041099485.1
          Length = 413

 Score =  547 bits (1410), Expect = e-160
 Identities = 288/411 (70%), Positives = 340/411 (82%), Gaps = 7/411 (1%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQK+GGTS+GS ERI  VA +V +++  G  LVVV+SAMSGETNRLI LAK +S  
Sbjct: 1   MALIVQKYGGTSMGSPERIRNVAKRVARWKAQGHQLVVVVSAMSGETNRLIALAKDVS-- 58

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP  RELDV++STGEQVTIALLAMA+   G+ A SYTG QV++LTDS  TKARIL+IDD
Sbjct: 59  PQPDARELDVMISTGEQVTIALLAMAIRDLGLKARSYTGGQVKVLTDSTFTKARILEIDD 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
             +R DL    V++VAGFQGVD  GNITTLGRGGSDT+ VA+AAAL ADECQIYTDVDGV
Sbjct: 119 ANMRRDLDDDTVIIVAGFQGVDADGNITTLGRGGSDTSAVAMAAALAADECQIYTDVDGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSF----KE 236
           YTTDPR+V  A++LD+ITFEEMLEMASLGSKVLQIR+VEFAGKY V LRVL SF    +E
Sbjct: 179 YTTDPRIVPEARKLDRITFEEMLEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFEEEGQE 238

Query: 237 GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMI 296
             GTLIT++E+ +MEQPIISGIAFNRDEAKLT+ GVPD PG+A++ILGPI+ ANI+VDMI
Sbjct: 239 TSGTLITLEEDTTMEQPIISGIAFNRDEAKLTVLGVPDRPGIAYQILGPIADANIDVDMI 298

Query: 297 VQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGVGMRSH 355
           +QNV HD TTDF+FTV+R+E+   +++L++  K  IGAR + GD KI KVS VGVGMRSH
Sbjct: 299 IQNVGHDGTTDFSFTVNRSEFARTKKLLEDQIKPHIGARAIEGDNKICKVSAVGVGMRSH 358

Query: 356 AGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406
            GVAS+MF  LA+E INIQMISTSEIK+SVV++EKYLELAVR LH  FELD
Sbjct: 359 PGVASKMFRTLAEEGINIQMISTSEIKISVVVDEKYLELAVRVLHKVFELD 409


Lambda     K      H
   0.316    0.133    0.357 

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: 559
Number of extensions: 14
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: 413
Length of database: 413
Length adjustment: 31
Effective length of query: 382
Effective length of database: 382
Effective search space:   145924
Effective search space used:   145924
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_041099485.1 SUTH_RS11835 (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.25116.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-135  437.1   7.5   3.7e-135  437.0   7.5    1.0  1  lcl|NCBI__GCF_000828635.1:WP_041099485.1  SUTH_RS11835 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000828635.1:WP_041099485.1  SUTH_RS11835 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.0   7.5  3.7e-135  3.7e-135       1     406 [.       1     408 [.       1     409 [. 0.96

  Alignments for each domain:
  == domain 1  score: 437.0 bits;  conditional E-value: 3.7e-135
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liVqK+GGts+gs eri+++ak+v + + +g++ vVVvSAms++t++l++la      + +s ++  
  lcl|NCBI__GCF_000828635.1:WP_041099485.1   1 MALIVQKYGGTSMGSPERIRNVAKRVARWKAQGHQLVVVVSAMSGETNRLIALA------KDVSPQPDA 63 
                                               579***************************************************......9******** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d ++s+GE++++all++a+r+lg ka++++g++  +lTd++f++A+i e++   ++   L++++++
  lcl|NCBI__GCF_000828635.1:WP_041099485.1  64 RELDVMISTGEQVTIALLAMAIRDLGLKARSYTGGQVKVLTDSTFTKARILEIDD-ANMRRDLDDDTVI 131
                                               ******************************************************9.9************ PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               +vaGF+G + +G+iTtLGRGGSD++A+++aaal Ad+++iyTDV+GvyttDPr+v+ea+k+d+i++eE+
  lcl|NCBI__GCF_000828635.1:WP_041099485.1 132 IVAGFQGVDADGNITTLGRGGSDTSAVAMAAALAADECQIYTDVDGVYTTDPRIVPEARKLDRITFEEM 200
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskeke....egTlitn....kkensslvkaialeknvar 268
                                               le+A+lG kvl+ r++e+a ++kv+++v ss+e+e    +gTlit     ++e++ ++++ia++++ a+
  lcl|NCBI__GCF_000828635.1:WP_041099485.1 201 LEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFEEEgqetSGTLITLeedtTMEQP-IISGIAFNRDEAK 268
                                               *******************************9875432569***98777667777.************* PP

                                 TIGR00656 269 ltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesg.aae 333
                                               ltv   g+ +++gi+ +i + +a+++i+vd+i+q  ++   t+ s++v++ +  ++kk+L+++ +  ++
  lcl|NCBI__GCF_000828635.1:WP_041099485.1 269 LTVL--GVPDRPGIAYQILGPIADANIDVDMIIQNVGHdgtTDFSFTVNRSEFARTKKLLEDQIKpHIG 335
                                               ****..9***************************9988888********************99752567 PP

                                 TIGR00656 334 lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhe 402
                                                + +e ++++++vs+vg+g++++pGvas++f  l+e++ini mis+se+kisv+vdek++e avr lh+
  lcl|NCBI__GCF_000828635.1:WP_041099485.1 336 ARAIEGDNKICKVSAVGVGMRSHPGVASKMFRTLAEEGINIQMISTSEIKISVVVDEKYLELAVRVLHK 404
                                               9******************************************************************** PP

                                 TIGR00656 403 klee 406
                                               ++e+
  lcl|NCBI__GCF_000828635.1:WP_041099485.1 405 VFEL 408
                                               **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (413 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: 11.55
//
[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