Alignments for a candidate for asp-kinase in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Trichormus variabilis ATCC 29413

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011320349.1 AVA_RS18465 aspartate kinase

Query= BRENDA::P74569
         (600 letters)



>NCBI__GCF_000204075.1:WP_011320349.1
          Length = 604

 Score =  808 bits (2086), Expect = 0.0
 Identities = 432/604 (71%), Positives = 503/604 (83%), Gaps = 6/604 (0%)

Query: 1   MALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPN 60
           MALIVQKFGG+SVG+VERIQAVAQR+ +TV+ GNSLVVVVSAMGK+TD LV LA +IS N
Sbjct: 1   MALIVQKFGGSSVGSVERIQAVAQRVYKTVKAGNSLVVVVSAMGKTTDGLVKLANEISRN 60

Query: 61  PCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDR 120
           P RREMDMLLSTGEQV+IALLS+ALQE+ QPAIS+TGAQVGIVTEAEH+RARIL I  +R
Sbjct: 61  PNRREMDMLLSTGEQVTIALLSMALQELGQPAISMTGAQVGIVTEAEHTRARILHIETER 120

Query: 121 LEHHLREGKVVVVAGFQGISSVEHLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGI 180
           +E H++EGKVVVVAGFQGISS   LEITTLGRGGSDTSAVALAAAL+ADFCEIYTDVPGI
Sbjct: 121 VEGHIQEGKVVVVAGFQGISSNGSLEITTLGRGGSDTSAVALAAALQADFCEIYTDVPGI 180

Query: 181 LTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGT 240
           LTTDPR+VPEAQLM EITC+EMLELASLGAKVLHPRAVEIARNYG+PLVV+SSW+D+PGT
Sbjct: 181 LTTDPRIVPEAQLMGEITCNEMLELASLGAKVLHPRAVEIARNYGMPLVVKSSWTDDPGT 240

Query: 241 KVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDID 300
            V  P  Q RSL+ LE+A+ VD VE D DQAKVALLRVPD+PGVA+KLF +I++Q+VD+D
Sbjct: 241 WVTTPKPQGRSLINLELARPVDDVELDTDQAKVALLRVPDKPGVAAKLFGEISRQKVDVD 300

Query: 301 LIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALR--SYPEADQEAEIIVEKGIAKI 358
           LIIQSIH+GNSNDIAFTV   +L  AEAV +AIAP+LR  S+P++D EAE++VE+ IAK+
Sbjct: 301 LIIQSIHEGNSNDIAFTVTTPILKRAEAVAAAIAPSLRSPSHPKSD-EAEVMVEQNIAKV 359

Query: 359 AIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGV 418
           +IAGAGMIGRPG+AAKMF TLA+ GVNI+MISTSEVKVSCVID +D DRAI AL  AF +
Sbjct: 360 SIAGAGMIGRPGVAAKMFTTLAEAGVNIQMISTSEVKVSCVIDAQDGDRAIIALRKAFEI 419

Query: 419 TL---SPPKNQTDTSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVDM 475
                SP      T + P VRGVALD +QA++AIR VPDRPGMAAQLF  LA+ NISVDM
Sbjct: 420 ETPLHSPTPPTLSTHNSPPVRGVALDLNQARLAIRQVPDRPGMAAQLFGILAQNNISVDM 479

Query: 476 IIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVGS 535
           IIQSQRCRI  G P RDIAF V   D   A+ +L  +  +     +V++ AIAKVSIVG+
Sbjct: 480 IIQSQRCRIVDGVPRRDIAFTVPRMDGETAQKLLCQVAPELGWGDVVLDSAIAKVSIVGA 539

Query: 536 GMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTKT 595
           GM+G PGVAA  F ALA+  INI+MIATSEIKISCVV Q++GV AL+  H+AF LAGT+ 
Sbjct: 540 GMVGQPGVAAKMFEALAKHQINIQMIATSEIKISCVVSQEQGVQALQVIHTAFELAGTEK 599

Query: 596 VTVP 599
             VP
Sbjct: 600 FVVP 603


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: 970
Number of extensions: 40
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: 604
Length adjustment: 37
Effective length of query: 563
Effective length of database: 567
Effective search space:   319221
Effective search space used:   319221
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_011320349.1 AVA_RS18465 (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.2995.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-165  536.9  10.2   3.7e-128  413.9   8.6    2.0  2  lcl|NCBI__GCF_000204075.1:WP_011320349.1  AVA_RS18465 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011320349.1  AVA_RS18465 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.9   8.6  3.7e-128  3.7e-128       1     405 [.       1     418 [.       1     420 [. 0.95
   2 !  122.8   0.0   9.2e-40   9.2e-40     250     406 ..     432     594 ..     424     595 .. 0.95

  Alignments for each domain:
  == domain 1  score: 413.9 bits;  conditional E-value: 3.7e-128
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liVqKFGG+svgs+eri+++a++v k++k g++ vVVvSAm+k+td lv+la      + is ++++
  lcl|NCBI__GCF_000204075.1:WP_011320349.1   1 MALIVQKFGGSSVGSVERIQAVAQRVYKTVKAGNSLVVVVSAMGKTTDGLVKLA------NEISRNPNR 63 
                                               579***************************************************......89******* PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re+d+l+s+GE++++alls+al+elg+ a++++g++ gi+T++e+++A+i +++t er++  ++eg++v
  lcl|NCBI__GCF_000204075.1:WP_011320349.1  64 REMDMLLSTGEQVTIALLSMALQELGQPAISMTGAQVGIVTEAEHTRARILHIET-ERVEGHIQEGKVV 131
                                               *******************************************************.************* PP

                                 TIGR00656 139 vvaGFiGateeG..eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisye 205
                                               vvaGF+G  ++G  eiTtLGRGGSD++A++laaal+Ad +eiyTDV+G++ttDPr+v+ea+ + +i+ +
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 132 VVAGFQGISSNGslEITTLGRGGSDTSAVALAAALQADFCEIYTDVPGILTTDPRIVPEAQLMGEITCN 200
                                               ***********96679***************************************************** PP

                                 TIGR00656 206 EalelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.........kkensslvkaialekn 265
                                               E+lelA+lGakvlhpra+e+a ++++p++v+ss   + gT +t          + e  ++v  + l+ +
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 201 EMLELASLGAKVLHPRAVEIARNYGMPLVVKSSWTDDPGTWVTTpkpqgrsliNLELARPVDDVELDTD 269
                                               *******************************************98877766555555599********* PP

                                 TIGR00656 266 varltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesga 331
                                               +a++++    + +k+g++a++f+ +++++++vdli+q+  e   ++i+++v +  +++a+++  +    
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 270 QAKVALL--RVPDKPGVAAKLFGEISRQKVDVDLIIQSIHEgnsNDIAFTVTTPILKRAEAVAAAIAPS 336
                                               ******9..*****************************9999999********9888888777666555 PP

                                 TIGR00656 332 ae........lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekd 392
                                               +           ++ ve+++a+vsi gag+++ pGva+++f+ l+e ++ni mis+se+k+s ++d +d
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 337 LRspshpksdEAEVMVEQNIAKVSIAGAGMIGRPGVAAKMFTTLAEAGVNIQMISTSEVKVSCVIDAQD 405
                                               5566778877889******************************************************** PP

                                 TIGR00656 393 aekavrklhekle 405
                                                 +a+ +l++++e
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 406 GDRAIIALRKAFE 418
                                               **********997 PP

  == domain 2  score: 122.8 bits;  conditional E-value: 9.2e-40
                                 TIGR00656 250 kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese........tsis 310
                                               +++ns++v+++al+ n+arl+++  ++ +++g++a++f++La+++i+vd+i+q++           +i+
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 432 STHNSPPVRGVALDLNQARLAIR--QVPDRPGMAAQLFGILAQNNISVDMIIQSQRCrivdgvprRDIA 498
                                               567788*****************..*****************************944788888889*** PP

                                 TIGR00656 311 lvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmiss 379
                                               ++v + d ++a+k+L ++  +++  ++ +++ +a+vsivgag+v++pGva+++f+al++++ini mi++
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 499 FTVPRMDGETAQKLLCQVAPELGWGDVVLDSAIAKVSIVGAGMVGQPGVAAKMFEALAKHQINIQMIAT 567
                                               ********************************************************************* PP

                                 TIGR00656 380 setkisvlvdekdaekavrklheklee 406
                                               se+kis +v++++ ++a + +h ++e+
  lcl|NCBI__GCF_000204075.1:WP_011320349.1 568 SEIKISCVVSQEQGVQALQVIHTAFEL 594
                                               ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (604 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.28
//
[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