Alignments for a candidate for asp-kinase in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012410916.1 NPUN_RS23210 aspartate kinase

Query= BRENDA::P74569
         (600 letters)



>NCBI__GCF_000020025.1:WP_012410916.1
          Length = 618

 Score =  791 bits (2042), Expect = 0.0
 Identities = 426/619 (68%), Positives = 500/619 (80%), Gaps = 20/619 (3%)

Query: 1   MALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPN 60
           MALIVQK+GGTSVG+VERIQAVAQR+ +TVQ GNSLVVVVSAMGK+TD LV LA +ISPN
Sbjct: 1   MALIVQKYGGTSVGSVERIQAVAQRVYKTVQAGNSLVVVVSAMGKTTDGLVKLANEISPN 60

Query: 61  PCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDR 120
           P RREMDMLLSTGEQV+IALLS+ALQE+ QPAIS+TGAQVGIVTEAEHSRARIL I   R
Sbjct: 61  PNRREMDMLLSTGEQVTIALLSMALQELGQPAISMTGAQVGIVTEAEHSRARILHIDTTR 120

Query: 121 LEHHLREGKVVVVAGFQGISSVEHLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGI 180
           L  H+  GKVVVVAGFQG SS   +EITTLGRGGSDTSAVA+AAAL+A+FCEIYTDVPGI
Sbjct: 121 LCRHINAGKVVVVAGFQGTSSTGEMEITTLGRGGSDTSAVAIAAALRANFCEIYTDVPGI 180

Query: 181 LTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGT 240
           LTTDPRLV EAQLM +ITCDEMLELASLGAKVLHPRAVEIARNYG+PLVVRSSW+D+PGT
Sbjct: 181 LTTDPRLVAEAQLMDDITCDEMLELASLGAKVLHPRAVEIARNYGVPLVVRSSWTDQPGT 240

Query: 241 KVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDID 300
            V +   Q RSL+ LEIA+ VD VE+D DQAKVALLRVPD+PGVA++LF +I++Q+VD+D
Sbjct: 241 WVTSAKPQGRSLINLEIARPVDAVEFDTDQAKVALLRVPDKPGVAARLFGEISRQKVDVD 300

Query: 301 LIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALR--SYPEADQEAEIIVEKGIAKI 358
           LIIQSIH+GNSNDIAFTV   +L  AEAV +AIAPALR  S P++D EAE+++E  IAK+
Sbjct: 301 LIIQSIHEGNSNDIAFTVTTPILKRAEAVAAAIAPALRNPSNPKSD-EAEVMLEHNIAKV 359

Query: 359 AIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGV 418
           +IAGAGMIGRPG+AAKMF TLA+ GVNI+MISTSEVKVSCV+D  + D A+ AL  AF +
Sbjct: 360 SIAGAGMIGRPGVAAKMFATLAEAGVNIQMISTSEVKVSCVVDAAECDHAVLALRTAFEI 419

Query: 419 TL---------------SPPK--NQTDTSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQ 461
                            SPP         + P VRGVALD +QA++AIR +PDRPGMAA+
Sbjct: 420 EAGEQGSRGAGESACIDSPPPLCPSAPLPNCPPVRGVALDLNQARLAIRQLPDRPGMAAK 479

Query: 462 LFTALAEANISVDMIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAI 521
           LF  LA+ NISVDMIIQSQRCR+  G P RDIAF V+  D+  A+ +L  +  +     +
Sbjct: 480 LFGLLAQHNISVDMIIQSQRCRVIDGVPRRDIAFTVSRIDAESAKKMLTQVAAELGWGEV 539

Query: 522 VVNKAIAKVSIVGSGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDAL 581
           V++ AIAKVSIVG+GM+G PGVAA  F ALAQ  INI+MIATSEIKISCVV Q++GV AL
Sbjct: 540 VLDSAIAKVSIVGAGMVGQPGVAAKMFEALAQHQINIQMIATSEIKISCVVAQEQGVKAL 599

Query: 582 KAAHSAFNLAGTKTVTVPA 600
           +A H+AF LAG++ V VPA
Sbjct: 600 QAIHAAFGLAGSEKVVVPA 618


Lambda     K      H
   0.318    0.132    0.366 

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: 981
Number of extensions: 36
Number of successful extensions: 14
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: 600
Length of database: 618
Length adjustment: 37
Effective length of query: 563
Effective length of database: 581
Effective search space:   327103
Effective search space used:   327103
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_012410916.1 NPUN_RS23210 (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.3153039.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-165  537.5  10.7   1.9e-128  414.9   8.3    2.0  2  NCBI__GCF_000020025.1:WP_012410916.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_012410916.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9   8.3  1.9e-128  1.9e-128       1     405 [.       1     418 [.       1     420 [. 0.95
   2 !  123.1   0.0   7.1e-40   7.1e-40     255     404 ..     451     606 ..     442     609 .. 0.96

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 1.9e-128
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + liVqK+GGtsvgs+eri+++a++v k+++ g++ vVVvSAm+k+td lv+la      + is ++++re+d
  NCBI__GCF_000020025.1:WP_012410916.1   1 MALIVQKYGGTSVGSVERIQAVAQRVYKTVQAGNSLVVVVSAMGKTTDGLVKLA------NEISPNPNRREMD 67 
                                           579***************************************************......8************ PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l+s+GE++++alls+al+elg+ a++++g++ gi+T++e+ +A+i +++t  rL   ++ g++vvvaGF+G+
  NCBI__GCF_000020025.1:WP_012410916.1  68 MLLSTGEQVTIALLSMALQELGQPAISMTGAQVGIVTEAEHSRARILHIDT-TRLCRHINAGKVVVVAGFQGT 139
                                           ***************************************************.********************9 PP

                             TIGR00656 147 teeG..eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakv 217
                                            + G  eiTtLGRGGSD++A+++aaal A+ +eiyTDV+G++ttDPr+v ea+ +d i+ +E+lelA+lGakv
  NCBI__GCF_000020025.1:WP_012410916.1 140 SSTGemEITTLGRGGSDTSAVAIAAALRANFCEIYTDVPGILTTDPRLVAEAQLMDDITCDEMLELASLGAKV 212
                                           88773369***************************************************************** PP

                             TIGR00656 218 lhpralelaveakvpilvrsskekeegTlitn.........kkensslvkaialeknvarltvegegmlgkrg 281
                                           lhpra+e+a +++vp++vrss   + gT +t+         + e  ++v a+ ++ ++a++++    + +k+g
  NCBI__GCF_000020025.1:WP_012410916.1 213 LHPRAVEIARNYGVPLVVRSSWTDQPGTWVTSakpqgrsliNLEIARPVDAVEFDTDQAKVALL--RVPDKPG 283
                                           ********************************8877766665556699***************9..******* PP

                             TIGR00656 282 ilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaae........lesleveedl 343
                                           ++a++f+ +++++++vdli+q+  e   ++i+++v +  +++a+++  +   a+           ++ +e+++
  NCBI__GCF_000020025.1:WP_012410916.1 284 VAARLFGEISRQKVDVDLIIQSIHEgnsNDIAFTVTTPILKRAEAVAAAIAPALRnpsnpksdEAEVMLEHNI 356
                                           **********************9999999********9999998888877777667788887788999***** PP

                             TIGR00656 344 avvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           a+vsi gag+++ pGva+++f+ l+e ++ni mis+se+k+s +vd ++  +av +l+ ++e
  NCBI__GCF_000020025.1:WP_012410916.1 357 AKVSIAGAGMIGRPGVAAKMFATLAEAGVNIQMISTSEVKVSCVVDAAECDHAVLALRTAFE 418
                                           **********************************************************9997 PP

  == domain 2  score: 123.1 bits;  conditional E-value: 7.1e-40
                             TIGR00656 255 slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese........tsislvvdeedvd 319
                                           ++v+++al+ n+arl+++  ++ +++g++a++f++La+++i+vd+i+q++           +i+++v++ d++
  NCBI__GCF_000020025.1:WP_012410916.1 451 PPVRGVALDLNQARLAIR--QLPDRPGMAAKLFGLLAQHNISVDMIIQSQRCrvidgvprRDIAFTVSRIDAE 521
                                           58****************..*****************************944788888889************ PP

                             TIGR00656 320 eakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekd 392
                                           +akk+L+++  +++  ++ +++ +a+vsivgag+v++pGva+++f+al++++ini mi++se+kis +v +++
  NCBI__GCF_000020025.1:WP_012410916.1 522 SAKKMLTQVAAELGWGEVVLDSAIAKVSIVGAGMVGQPGVAAKMFEALAQHQINIQMIATSEIKISCVVAQEQ 594
                                           ************************************************************************* PP

                             TIGR00656 393 aekavrklhekl 404
                                            +ka +++h+++
  NCBI__GCF_000020025.1:WP_012410916.1 595 GVKALQAIHAAF 606
                                           *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (618 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: 00:00:00.00
# Mc/sec: 32.99
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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