Alignments for a candidate for asp-kinase in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Synechococcus elongatus PCC 7942

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Synpcc7942_1001 Synpcc7942_1001 aspartate kinase

Query= BRENDA::P74569
         (600 letters)



>FitnessBrowser__SynE:Synpcc7942_1001
          Length = 616

 Score =  703 bits (1814), Expect = 0.0
 Identities = 392/606 (64%), Positives = 459/606 (75%), Gaps = 15/606 (2%)

Query: 1   MALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPN 60
           MALIVQK+GGTSVG+VERI AVAQRI +TV  GN +VVVVSAMG STD L+ LA  IS N
Sbjct: 20  MALIVQKYGGTSVGSVERITAVAQRIAQTVAAGNQVVVVVSAMGHSTDELLKLANAISAN 79

Query: 61  PCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDR 120
           P RRE+DMLL+TGEQVSIALLS+AL E    AIS+TGAQVGI+TEA HSRARILEI P R
Sbjct: 80  PSRRELDMLLATGEQVSIALLSMALHEQGCDAISMTGAQVGIITEAHHSRARILEIDPQR 139

Query: 121 LEHHLREGKVVVVAGFQGISSVEH---LEITTLGRGGSDTSAVALAAALKADFCEIYTDV 177
           L+  L  G+VVVVAGFQGI+S +     EITTLGRGGSDTSAVALAAAL AD CEIYTDV
Sbjct: 140 LQSQLDAGRVVVVAGFQGIASSDRTALTEITTLGRGGSDTSAVALAAALNADRCEIYTDV 199

Query: 178 PGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDE 237
           PGILTTDPRLVPEA L+ EITCDEMLELASLGA VLHPRAVEIARNYG+ LVVRSSW+ E
Sbjct: 200 PGILTTDPRLVPEAHLLEEITCDEMLELASLGASVLHPRAVEIARNYGVRLVVRSSWTQE 259

Query: 238 PGTKVVAPPVQ-NRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQ 296
           PGT VVAPP + +RSL GLEI + VDG+  D DQAKVALL VPDRPG+A+ LF ++AQ+ 
Sbjct: 260 PGTGVVAPPRRSDRSLQGLEIGRPVDGLALDTDQAKVALLHVPDRPGIAASLFGEMAQRG 319

Query: 297 VDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIA 356
           V++DLIIQSIH+GNSNDI+FTV +  L  AEA T+ +         AD   E   E  +A
Sbjct: 320 VNVDLIIQSIHEGNSNDISFTVSQADLEKAEAGTTQLL--------ADLGGEQQSEAAVA 371

Query: 357 KIAIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAF 416
           K++I+G G++GRPGIAA+MF  LA  G+NI+MISTSEVKVSCVI   D  RAIAAL  +F
Sbjct: 372 KVSISGVGIVGRPGIAAQMFSALAQGGINIQMISTSEVKVSCVIAAADQQRAIAALQESF 431

Query: 417 GVTLSPPKNQTD--TSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVD 474
            +  +     TD  T+ LPAVRGVALD+DQA++AI +VPD PGMAA +F  LA+  ISVD
Sbjct: 432 ELEEAIAATATDACTTDLPAVRGVALDRDQARLAILNVPDLPGMAATIFQILADRQISVD 491

Query: 475 MIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVG 534
           MIIQSQR RI+ G PCRDIA  +   D+  A A LQ    D    ++ +   IAKVSIVG
Sbjct: 492 MIIQSQRGRIHNGQPCRDIACTLPPADAELAAAALQ-AFADQHGCSLEIQTEIAKVSIVG 550

Query: 535 SGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTK 594
           SGM+  PGVAA  FAALA   INI MIATSEIK+SC+V   + V+AL+  H+AF LA  +
Sbjct: 551 SGMVQQPGVAAQMFAALANHGINIHMIATSEIKVSCIVDASQAVEALQTVHAAFGLASDR 610

Query: 595 TVTVPA 600
            + VPA
Sbjct: 611 RIEVPA 616


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: 965
Number of extensions: 35
Number of successful extensions: 17
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: 616
Length adjustment: 37
Effective length of query: 563
Effective length of database: 579
Effective search space:   325977
Effective search space used:   325977
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 Synpcc7942_1001 Synpcc7942_1001 (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.15118.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-165  535.5  14.0   1.4e-131  425.2   8.5    2.0  2  lcl|FitnessBrowser__SynE:Synpcc7942_1001  Synpcc7942_1001 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1001  Synpcc7942_1001 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.2   8.5  1.4e-131  1.4e-131       1     406 [.      20     433 ..      20     434 .. 0.95
   2 !  113.7   0.2   5.2e-37   5.2e-37     255     404 ..     450     604 ..     436     607 .. 0.94

  Alignments for each domain:
  == domain 1  score: 425.2 bits;  conditional E-value: 1.4e-131
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liVqK+GGtsvgs+eri ++a+++ +++  g++vvVVvSAm+++tdel++la      +ais ++s+
  lcl|FitnessBrowser__SynE:Synpcc7942_1001  20 MALIVQKYGGTSVGSVERITAVAQRIAQTVAAGNQVVVVVSAMGHSTDELLKLA------NAISANPSR 82 
                                               579***************************************************......8******** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d+l+++GE++s+alls+al+e+g +a++++g++ gi+T++++ +A+i e+++ +rL ++L+ g +v
  lcl|FitnessBrowser__SynE:Synpcc7942_1001  83 RELDMLLATGEQVSIALLSMALHEQGCDAISMTGAQVGIITEAHHSRARILEIDP-QRLQSQLDAGRVV 150
                                               *******************************************************.************* PP

                                 TIGR00656 139 vvaGFiG.....ateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidki 202
                                               vvaGF+G     +t   eiTtLGRGGSD++A++laaal+Adr+eiyTDV+G++ttDPr+v+ea+ +++i
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 151 VVAGFQGiassdRTALTEITTLGRGGSDTSAVALAAALNADRCEIYTDVPGILTTDPRLVPEAHLLEEI 219
                                               *******54433355689*************************************************** PP

                                 TIGR00656 203 syeEalelAtlGakvlhpralelaveakvpilvrsskekeegTlitn......kkens.......slvk 258
                                               + +E+lelA+lGa vlhpra+e+a +++v ++vrss  +e gT +++      +   s       ++v 
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 220 TCDEMLELASLGASVLHPRAVEIARNYGVRLVVRSSWTQEPGTGVVApprrsdR---SlqgleigRPVD 285
                                               **********************************************98876651...2445566699** PP

                                 TIGR00656 259 aialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakka 324
                                               ++al+ ++a++++   ++ +++gi+a +f+ +a++++nvdli+q+  e   ++is++v++ d+++a++ 
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 286 GLALDTDQAKVALL--HVPDRPGIAASLFGEMAQRGVNVDLIIQSIHEgnsNDISFTVSQADLEKAEAG 352
                                               *************9..9****************************9999999**************998 PP

                                 TIGR00656 325 LkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekda 393
                                                ++   +++  + + e  +a+vsi+g+g+v+ pG+a+++f+al++ +ini mis+se+k+s ++  +d 
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 353 TTQLLADLG-GEQQSEAAVAKVSISGVGIVGRPGIAAQMFSALAQGGINIQMISTSEVKVSCVIAAADQ 420
                                               888877777.66778899*************************************************** PP

                                 TIGR00656 394 ekavrklheklee 406
                                               ++a+ +l+e++e+
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 421 QRAIAALQESFEL 433
                                               **********987 PP

  == domain 2  score: 113.7 bits;  conditional E-value: 5.2e-37
                                 TIGR00656 255 slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese........tsislvvde 315
                                               + v+++al++++arl++   ++ + +g++a+if++La+++i+vd+i+q++           +i+ ++  
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 450 PAVRGVALDRDQARLAIL--NVPDLPGMAATIFQILADRQISVDMIIQSQRGrihngqpcRDIACTLPP 516
                                               489***************..****************************9944788899999******** PP

                                 TIGR00656 316 edvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetki 384
                                                d++ a +aL+++ ++ + +sle++ ++a+vsivg+g+v++pGva+++f+al++++ini mi++se+k+
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 517 ADAELAAAALQAFADQHG-CSLEIQTEIAKVSIVGSGMVQQPGVAAQMFAALANHGINIHMIATSEIKV 584
                                               *************98888.************************************************** PP

                                 TIGR00656 385 svlvdekdaekavrklhekl 404
                                               s +vd  +a++a +++h+++
  lcl|FitnessBrowser__SynE:Synpcc7942_1001 585 SCIVDASQAVEALQTVHAAF 604
                                               *****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (616 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: 10.68
//
[ok]

This GapMind analysis is from Apr 09 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