Alignments for a candidate for asp-kinase in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Persephonella marina EX-H1

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012675675.1 PERMA_RS08105 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000021565.1:WP_012675675.1
          Length = 410

 Score =  446 bits (1146), Expect = e-130
 Identities = 233/403 (57%), Positives = 308/403 (76%), Gaps = 3/403 (0%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           M LIVQKFGGTSVGS+ERI+ VA+K+K+  + G+ +VVV SAM+GET+RL+ L + +S  
Sbjct: 1   MPLIVQKFGGTSVGSIERIKNVANKIKRAVEEGNKVVVVSSAMAGETDRLLTLTRELSS- 59

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            +P PRE D++VSTGEQV I L+++AL + G+ AVS TG QV I TD AHTKARI +ID 
Sbjct: 60  -KPDPREQDMVVSTGEQVAIGLISIALKEMGIDAVSLTGWQVPIYTDDAHTKARIKKIDT 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
            +I ++L  GRVV+VAGFQG+ + G+ITTLGRGGSDTT VALAAAL AD C+IYTDV GV
Sbjct: 119 GRILSELDKGRVVIVAGFQGISDYGDITTLGRGGSDTTAVALAAALNADVCEIYTDVTGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240
           +T DPR+V  A+++  I++EEM+EMASLGSKV+QIR+VEFA KY V + V  SF E  GT
Sbjct: 179 FTADPRIVENAKKIPVISYEEMMEMASLGSKVMQIRSVEFAAKYGVKIHVKSSFIEEDGT 238

Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300
            I ++E E ME+ ++ GI+ +  E+++T+  VPD PG+A K+   +   NI VDMIVQNV
Sbjct: 239 WI-VEENEEMEKVVVRGISHDLKESRITVVQVPDKPGIAAKLFKALGDRNIVVDMIVQNV 297

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
           SH+  TD +FTV++ + + AE I +  AKEIGA+ V  + +IAK+S+VG+GM++HAG A 
Sbjct: 298 SHEGYTDISFTVNKIDAEYAEEIAKEVAKEIGAKGVERNDRIAKISVVGLGMKTHAGTAG 357

Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403
           +MFE L +E INI  ISTSEIK+S +I+EKY ELAVRALH AF
Sbjct: 358 KMFEVLYREGINIYAISTSEIKISCLIDEKYAELAVRALHEAF 400


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: 469
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: 410
Length adjustment: 31
Effective length of query: 382
Effective length of database: 379
Effective search space:   144778
Effective search space used:   144778
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_012675675.1 PERMA_RS08105 (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.1392475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-138  448.7  15.1   1.1e-138  448.5  15.1    1.0  1  NCBI__GCF_000021565.1:WP_012675675.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021565.1:WP_012675675.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.5  15.1  1.1e-138  1.1e-138       2     406 ..       2     402 ..       1     403 [. 0.98

  Alignments for each domain:
  == domain 1  score: 448.5 bits;  conditional E-value: 1.1e-138
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 
                                            liVqKFGGtsvgs+erik++a++++++++eg+kvvVV SAm+++td+l++l+      +  s+++ pre+d+
  NCBI__GCF_000021565.1:WP_012675675.1   2 PLIVQKFGGTSVGSIERIKNVANKIKRAVEEGNKVVVVSSAMAGETDRLLTLT------RELSSKPDPREQDM 68 
                                           59***************************************************......899*********** PP

                             TIGR00656  75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147
                                           +vs+GE++++ l+s al+e g +a++l+g++ +i Tdd +++A+ik+++t  r+l+ L++g +v+vaGF+G  
  NCBI__GCF_000021565.1:WP_012675675.1  69 VVSTGEQVAIGLISIALKEMGIDAVSLTGWQVPIYTDDAHTKARIKKIDT-GRILSELDKGRVVIVAGFQGIS 140
                                           **************************************************.********************** PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                             G+iTtLGRGGSD+tA++laaal+Ad +eiyTDV Gv+t+DPr+ve+akki+ isyeE++e+A+lG kv++ 
  NCBI__GCF_000021565.1:WP_012675675.1 141 DYGDITTLGRGGSDTTAVALAAALNADVCEIYTDVTGVFTADPRIVENAKKIPVISYEEMMEMASLGSKVMQI 213
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskekeegTlitnkkens..slvkaialeknvarltvegegmlgkrgilaeifkaLa 291
                                           r++e+a +++v+i v+ss+ +e+gT i++++e+    +v++i+++ + +r+tv+  ++ +k+gi+a++fkaL+
  NCBI__GCF_000021565.1:WP_012675675.1 214 RSVEFAAKYGVKIHVKSSFIEEDGTWIVEENEEMekVVVRGISHDLKESRITVV--QVPDKPGIAAKLFKALG 284
                                           ****************************9444333469****************..***************** PP

                             TIGR00656 292 eeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvas 361
                                           +++i vd+i+q  s+   t+is++v++ d++ a+++ ke+ ++++ + +e +  +a++s+vg g++ + G a+
  NCBI__GCF_000021565.1:WP_012675675.1 285 DRNIVVDMIVQNVSHegyTDISFTVNKIDAEYAEEIAKEVAKEIGAKGVERNDRIAKISVVGLGMKTHAGTAG 357
                                           ***********9998899******************************************************* PP

                             TIGR00656 362 eifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           ++f++l  ++ini  is+se+kis l+dek+ae avr+lhe+++e
  NCBI__GCF_000021565.1:WP_012675675.1 358 KMFEVLYREGINIYAISTSEIKISCLIDEKYAELAVRALHEAFIE 402
                                           *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (410 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 15.78
//
[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