Alignments for a candidate for asp-kinase in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Alkalihalobacterium alkalinitrilicum DSM 22532

Align aspartokinase I (alpha and beta subunits) (EC 2.7.2.4) (characterized)
to candidate WP_078430740.1 BK574_RS26660 aspartate kinase

Query= metacyc::BSU16760-MONOMER
         (404 letters)



>NCBI__GCF_002019605.1:WP_078430740.1
          Length = 414

 Score =  521 bits (1343), Expect = e-152
 Identities = 267/404 (66%), Positives = 325/404 (80%), Gaps = 2/404 (0%)

Query: 1   MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60
           MK+IVQKFGGTSVK+++ R++A  H+++++++GYKVVVVVSAMGR GDPYATD+LL L+ 
Sbjct: 1   MKVIVQKFGGTSVKNEEVRRMAARHVQKSVNDGYKVVVVVSAMGRSGDPYATDTLLNLI- 59

Query: 61  GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120
            ++  +  REQDLLLSCGE ISSVVFT +L   GV A A+TGAQAGF TN+  ++AKIIE
Sbjct: 60  -NKKTVPKREQDLLLSCGEIISSVVFTDLLSSYGVTAKAMTGAQAGFRTNEDFSSAKIIE 118

Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180
           MK E+L   L   DAVVVAGFQG ++ G+ TT+GRGGSDTSA A+GAA+ AE++DIFTDV
Sbjct: 119 MKCEKLMKTLEKVDAVVVAGFQGQSKTGEITTLGRGGSDTSATAIGAALGAEWVDIFTDV 178

Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240
           EGVMTADPR+VE A+PL VVTY EICN+AYQGAKVI PRAVEIAMQAK+PI +RSTYS+ 
Sbjct: 179 EGVMTADPRIVEGARPLSVVTYNEICNMAYQGAKVIHPRAVEIAMQAKIPIHIRSTYSDS 238

Query: 241 KGTLVTSHHSSKVGSDVFERLITGIAHVKDVTQFKVPAKIGQYNVQTEVFKAMANAGISV 300
           KGTLVTS    + G DV +RLITGIAH+  VTQ KV AK GQY++Q +VFKAMAN  ISV
Sbjct: 239 KGTLVTSMVGDQQGQDVQDRLITGIAHLAKVTQIKVLAKEGQYDLQEKVFKAMANERISV 298

Query: 301 DFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSKIV 360
           DF NI P  +VYTV     + A  +L  M Y+P VTR CAK+SAVGAG+ GVPGVT+KIV
Sbjct: 299 DFININPLGVVYTVMEEVADRAVEVLEQMNYEPQVTRRCAKISAVGAGMTGVPGVTAKIV 358

Query: 361 SALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEVFELSK 404
           +ALS++ + ILQSADSHTTIWVLV   DMV AVNALH++F+L K
Sbjct: 359 AALSKENVQILQSADSHTTIWVLVKGEDMVKAVNALHDMFQLEK 402


Lambda     K      H
   0.316    0.131    0.364 

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: 529
Number of extensions: 11
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: 404
Length of database: 414
Length adjustment: 31
Effective length of query: 373
Effective length of database: 383
Effective search space:   142859
Effective search space used:   142859
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_078430740.1 BK574_RS26660 (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.3141424.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-139  449.3  14.7   7.8e-139  449.1  14.7    1.0  1  NCBI__GCF_002019605.1:WP_078430740.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430740.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.1  14.7  7.8e-139  7.8e-139       1     406 [.       1     400 [.       1     401 [. 0.97

  Alignments for each domain:
  == domain 1  score: 449.1 bits;  conditional E-value: 7.8e-139
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           +++iVqKFGGtsv++ e ++ aa++v k++++g+kvvVVvSAm++++d +++ + ll+l++  ++ + +re+d
  NCBI__GCF_002019605.1:WP_078430740.1   1 MKVIVQKFGGTSVKNEEVRRMAARHVQKSVNDGYKVVVVVSAMGRSGDPYATDT-LLNLIN--KKTVPKREQD 70 
                                           689***************************************************.888875..56789***** PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l+s+GE +ss++++ +l  +gv a+a++g++ag++T++ f +Aki e++  e+L++ Le+ ++vvvaGF+G+
  NCBI__GCF_002019605.1:WP_078430740.1  71 LLLSCGEIISSVVFTDLLSSYGVTAKAMTGAQAGFRTNEDFSSAKIIEMKC-EKLMKTLEKVDAVVVAGFQGQ 142
                                           ***************************************************.********************* PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                            + GeiTtLGRGGSD++A++++aal A+ v+i+TDVeGv+t+DPr+ve a+++  ++y+E++++A++Gakv+h
  NCBI__GCF_002019605.1:WP_078430740.1 143 SKTGEITTLGRGGSDTSATAIGAALGAEWVDIFTDVEGVMTADPRIVEGARPLSVVTYNEICNMAYQGAKVIH 215
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.......kkensslvkaialeknvarltvegegmlgkrgilae 285
                                           pra+e+a++ak+pi +rs+++ ++gTl+t+       +  +++l+++ia+  +v++++v   ++ g++ ++ +
  NCBI__GCF_002019605.1:WP_078430740.1 216 PRAVEIAMQAKIPIHIRSTYSDSKGTLVTSmvgdqqgQDVQDRLITGIAHLAKVTQIKVL--AKEGQYDLQEK 286
                                           ******************************9997665555559*****************..99********* PP

                             TIGR00656 286 ifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapG 358
                                           +fka+a+e+i+vd+i++ +    + ++v ee +d+a+++L+++  +      +v + +a++s+vgag++++pG
  NCBI__GCF_002019605.1:WP_078430740.1 287 VFKAMANERISVDFININP--LGVVYTVMEEVADRAVEVLEQMNYE-----PQVTRRCAKISAVGAGMTGVPG 352
                                           *******************..**********************733.....358889**************** PP

                             TIGR00656 359 vaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           v+++i++al+++n++il++++s+t+i+vlv+++d++kav++lh+ +++
  NCBI__GCF_002019605.1:WP_078430740.1 353 VTAKIVAALSKENVQILQSADSHTTIWVLVKGEDMVKAVNALHDMFQL 400
                                           ********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (414 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.68
//
[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