Alignments for a candidate for asp-kinase in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Crocosphaera subtropica ATCC 51142

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_009543435.1 CCE_RS21240 aspartate kinase

Query= BRENDA::P74569
         (600 letters)



>NCBI__GCF_000017845.1:WP_009543435.1
          Length = 599

 Score =  826 bits (2133), Expect = 0.0
 Identities = 441/601 (73%), Positives = 503/601 (83%), Gaps = 3/601 (0%)

Query: 1   MALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPN 60
           MALIVQK+GGTSVG+VERIQ VAQRI++TVQ GN++VVVVSAMGK+TD LV LAQ+I+ N
Sbjct: 1   MALIVQKYGGTSVGSVERIQTVAQRIQKTVQQGNTVVVVVSAMGKTTDTLVSLAQEITAN 60

Query: 61  PCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDR 120
           P RREMDMLLSTGEQV+IAL+++ALQEI Q AISLTGAQVGIVTEAE+SRARIL I+PDR
Sbjct: 61  PSRREMDMLLSTGEQVTIALMTMALQEIGQAAISLTGAQVGIVTEAEYSRARILSIKPDR 120

Query: 121 LEHHLREGKVVVVAGFQGISSVEHLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGI 180
           ++ HL + +VVVVAGFQGISS E+LEITTLGRGGSDTSAVALAAALKA FCEIYTDVPGI
Sbjct: 121 IKRHLDKAEVVVVAGFQGISSRENLEITTLGRGGSDTSAVALAAALKASFCEIYTDVPGI 180

Query: 181 LTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGT 240
           LTTDPR+VPEA+LM EITCDEMLELASLGAKVLHPRAVEIARNYG+ LVVRSSWSD PGT
Sbjct: 181 LTTDPRIVPEARLMDEITCDEMLELASLGAKVLHPRAVEIARNYGVRLVVRSSWSDAPGT 240

Query: 241 KVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDID 300
            V++P  + RSL GLEIAKAVD VE+D +QAK+ALLRVPDRPG+A++LF +IA QQVD+D
Sbjct: 241 SVISPIPKPRSLEGLEIAKAVDAVEFDGEQAKIALLRVPDRPGIAARLFGEIAHQQVDVD 300

Query: 301 LIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIAKIAI 360
           LIIQSIH+GNSNDIAFTV+ ++L  AEAV  AIAPALR+ P    EAE++VE G+AKI+I
Sbjct: 301 LIIQSIHEGNSNDIAFTVINNVLTKAEAVAEAIAPALRTTPSNVTEAEVMVETGVAKISI 360

Query: 361 AGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGVTL 420
           AGAGMIGRPGIAA MFKTLA+  +NIEMISTSEVKVSCV+ + D DRAI  L  AF V L
Sbjct: 361 AGAGMIGRPGIAATMFKTLAEANINIEMISTSEVKVSCVVAKEDGDRAIKVLCEAFDVEL 420

Query: 421 SP-PKNQTDTSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVDMIIQS 479
           SP P         P VRGVALDQ QAQIAIRHV D+PGMAA +F  LAE NISVD IIQS
Sbjct: 421 SPNPVASQAVEVSPPVRGVALDQKQAQIAIRHVKDKPGMAASIFGVLAENNISVDTIIQS 480

Query: 480 QRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVGSGMIG 539
           QRCRI  G P RDIAF V EGD+  A  +L  L  D  D  ++V++ IAKVSIVG+GM+G
Sbjct: 481 QRCRILDGMPTRDIAFTVCEGDAKAACQVLSSL-SDGFD-EVIVDEDIAKVSIVGAGMVG 538

Query: 540 HPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTKTVTVP 599
            PGVAA FF ALA ENINI+MIATSEIKISCVVP+++GV ALKA H AF LAG + V V 
Sbjct: 539 QPGVAAKFFGALATENINIKMIATSEIKISCVVPKEQGVKALKAVHQAFELAGIEKVEVS 598

Query: 600 A 600
           A
Sbjct: 599 A 599


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: 956
Number of extensions: 37
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: 599
Length adjustment: 37
Effective length of query: 563
Effective length of database: 562
Effective search space:   316406
Effective search space used:   316406
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_009543435.1 CCE_RS21240 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.30634.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-179  583.7  21.8   6.2e-139  449.8  15.6    3.0  2  lcl|NCBI__GCF_000017845.1:WP_009543435.1  CCE_RS21240 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009543435.1  CCE_RS21240 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.8  15.6  6.2e-139  6.2e-139       1     440 [.       1     416 [.       1     418 [. 0.97
   2 !  128.6   0.4   1.8e-41   1.8e-41     288     441 ..     430     588 ..     423     589 .. 0.92

  Alignments for each domain:
  == domain 1  score: 449.8 bits;  conditional E-value: 6.2e-139
                                 TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 
                                               maliVqK+GGtSvg+veri+ va++++k+ ++gn vvVVvSAm+++Td Lv+la+++  ++        
  lcl|NCBI__GCF_000017845.1:WP_009543435.1   1 MALIVQKYGGTSVGSVERIQTVAQRIQKTVQQGNTVVVVVSAMGKTTDTLVSLAQEITANP-------- 61 
                                               89***********************************************************........ PP

                                 TIGR00657  70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138
                                                           s                    +re+d++ls+GE++++al+++al+e g+ a+sl+ga
  lcl|NCBI__GCF_000017845.1:WP_009543435.1  62 ------------S--------------------RREMDMLLSTGEQVTIALMTMALQEIGQAAISLTGA 98 
                                               ............5....................8*********************************** PP

                                 TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGat..ekgeittLGRGGSDltAallAaal 205
                                               + gi+t++e++rA+ + +ik +r++ +l++  +vvvaGF+G++  e+ eittLGRGGSD++A++lAaal
  lcl|NCBI__GCF_000017845.1:WP_009543435.1  99 QVGIVTEAEYSRAR-ILSIKPDRIKRHLDKAEVVVVAGFQGISsrENLEITTLGRGGSDTSAVALAAAL 166
                                               **************.**************************9988999********************* PP

                                 TIGR00657 206 kAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfn 274
                                               kA+ +eiytDV+Gi+t+DPrivpeAr++dei+++E+lELaslGakvLhpr++e+a+++++++vv+s+++
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 167 KASFCEIYTDVPGILTTDPRIVPEARLMDEITCDEMLELASLGAKVLHPRAVEIARNYGVRLVVRSSWS 235
                                               ********************************************************************* PP

                                 TIGR00657 275 peaeGTlivaksk.......seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlil 336
                                               +  +GT ++++          e ++av+a+++d +qa++++ +++++pgi+a++fg +a+++v+vdli+
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 236 DA-PGTSVISPIPkprslegLEIAKAVDAVEFDGEQAKIALLRVPDRPGIAARLFGEIAHQQVDVDLII 303
                                               99.***9998876789999988899******************************************** PP

                                 TIGR00657 337 qsssets...isfvvdkedadkakellk......kkvkeekaleevevekklalvslvGagmksapgva 396
                                               qs++e +   i+f+v ++ + ka+++ +      ++  ++    ev ve+++a++s+ Gagm+++pg+a
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 304 QSIHEGNsndIAFTVINNVLTKAEAVAEaiapalRTTPSNVTEAEVMVETGVAKISIAGAGMIGRPGIA 372
                                               ****555569***********99999889999998889999999************************* PP

                                 TIGR00657 397 akifeaLaeeniniemissseikisvvvdekdaekavealhekl 440
                                               a++f++Lae+niniemis+se+k+s+vv ++d+++a+++l e++
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 373 ATMFKTLAEANINIEMISTSEVKVSCVVAKEDGDRAIKVLCEAF 416
                                               ****************************************9987 PP

  == domain 2  score: 128.6 bits;  conditional E-value: 1.8e-41
                                 TIGR00657 288 seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsss....ets.....isfv 347
                                               +e +p+v++++ld++qa ++++ +++kpg++a +fg lae++++vd+i+qs+       +     i+f+
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 430 VEVSPPVRGVALDQKQAQIAIRHVKDKPGMAASIFGVLAENNISVDTIIQSQRcrilD-GmptrdIAFT 497
                                               566799*******************************************999976651.255567**** PP

                                 TIGR00657 348 vdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemisss 416
                                               v + da++a ++l+      + + ev v++++a+vs+vGagm+++pgvaak+f aLa enini+mi++s
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 498 VCEGDAKAACQVLS---SLSDGFDEVIVDEDIAKVSIVGAGMVGQPGVAAKFFGALATENINIKMIATS 563
                                               ************85...4678999********************************************* PP

                                 TIGR00657 417 eikisvvvdekdaekavealheklv 441
                                               eikis+vv++++++ka++a+h++++
  lcl|NCBI__GCF_000017845.1:WP_009543435.1 564 EIKISCVVPKEQGVKALKAVHQAFE 588
                                               **********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (599 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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.07
# Mc/sec: 3.36
//
[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