Alignments for a candidate for asp-kinase in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Chlorobium limicola DSM 245

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012467218.1 CLIM_RS11700 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Cola:Echvi_2000
         (815 letters)



>NCBI__GCF_000020465.1:WP_012467218.1
          Length = 822

 Score =  679 bits (1751), Expect = 0.0
 Identities = 364/821 (44%), Positives = 523/821 (63%), Gaps = 9/821 (1%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           MKI KFGGSS+ +   I+K+  II    + +   +V SAF  VT+ LL+ AN+A    E 
Sbjct: 1   MKIYKFGGSSLGSAARIKKIAGIIRSGLQPDCPVVVVSAFHRVTDLLLEAANVACTGREG 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALT-FVKVRFNELGDLFHGIYLIKECSNRTMDY 119
           Y  IL ++ + H  ++  L         L+  ++V   EL DL HG++L++E S ++   
Sbjct: 61  YLRILDDIGQLHKTVLDGLFSGSDAYAGLSDSIRVELAELHDLLHGVFLLRELSEKSTAL 120

Query: 120 VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179
           +LSFGERLS  I+A  L    +   Y+DAR+L+ TD  +G A V+ + T + I +     
Sbjct: 121 LLSFGERLSARIVAGYLNLLKLPAVYLDARELIVTDANYGSATVDLEETFQRIVNAPVPD 180

Query: 180 DDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239
             I V+TG+I +   G TTT+GR GSDYTAS+F AALGAE++ IWTDV G  +ADP+ V 
Sbjct: 181 GVIPVVTGYIAAAGDGTTTTLGRGGSDYTASLFGAALGAEEIFIWTDVDGFFSADPKRVR 240

Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGE 299
            A  +P +SY EAMELSH GAKV+ P T+ PAMK  IP+ IKN+F PD  GTRI ++   
Sbjct: 241 DARVLPFISYAEAMELSHAGAKVLHPFTILPAMKASIPVLIKNSFNPDAPGTRIERELDP 300

Query: 300 GKI-----IKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHS 354
             +     + G+SS++++ +LN+ G G+V V G++ R F  LA + IN+I ISQASSE S
Sbjct: 301 VAVRQIHPVTGLSSINSVVLLNLSGSGMVGVPGIASRLFSCLAKHHINVIFISQASSEQS 360

Query: 355 ICVAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMF 414
           I +AI    A++A  ++E+EF  E+Q+  +D + +   +A++AVVG NM  +PG S ++F
Sbjct: 361 ISLAINPAQAAKANRILEDEFAAEMQARLIDPLVLRRHLALVAVVGNNMSGHPGVSAQLF 420

Query: 415 QALGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLI 474
           + LG+N +NV A+AQG++E+NIS VI   D  KALN +HE+FFLS  KV H+FL G G I
Sbjct: 421 ETLGKNGINVIAVAQGANEMNISVVIDNRDEDKALNCIHESFFLSQRKV-HVFLAGTGTI 479

Query: 475 GKALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEP--MDM 532
            K+L + I +   NL+ E  LD+ + G+AN+R +   ++G DL       +  EP    +
Sbjct: 480 AKSLIRQISRHRMNLRREKDLDVLVCGLANTRRIAHADEGIDLDRWEDALKPREPGYAGI 539

Query: 533 DKFIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKK 592
           + +I  + E N  N+VFVDCTAS +VA+ Y ++L + + +VT NK   +G  E Y++++ 
Sbjct: 540 EGYIRLIRERNLHNTVFVDCTASGNVAEQYPELLRANISVVTANKLGMAGCAELYEQIRT 599

Query: 593 LAGQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFS 652
                  RF YETNV AGLP+INTL DL  SGD++  IE VLSG++++IF+EL KG  FS
Sbjct: 600 AQRVSNARFLYETNVGAGLPIINTLNDLKNSGDNIISIEGVLSGTLSFIFNELRKGGRFS 659

Query: 653 EVVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAAS 712
           ++V  AKE GYTEPDPRDDLSG D ARK+LILGRE G  + + DVE +S+VPE+      
Sbjct: 660 DIVRMAKEAGYTEPDPRDDLSGADFARKVLILGRELGCPMIYSDVECESLVPEELRGEMP 719

Query: 713 VPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSD 772
           V EF  +L   D  + + +  A   G  + +   + +GKA +G+  +    P   L GS+
Sbjct: 720 VEEFLGRLSSVDRWYAEEIQTAGKAGMTIAYAGEIRDGKASIGVKRVPLSSPIAGLNGSE 779

Query: 773 NMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813
           NM++FTT+RYN  P++VRGPGAG +VTA GVFADI+R+ +Y
Sbjct: 780 NMVVFTTDRYNITPLVVRGPGAGGEVTAGGVFADILRIASY 820


Lambda     K      H
   0.317    0.134    0.375 

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: 1397
Number of extensions: 64
Number of successful extensions: 7
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: 815
Length of database: 822
Length adjustment: 41
Effective length of query: 774
Effective length of database: 781
Effective search space:   604494
Effective search space used:   604494
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: 56 (26.2 bits)

Align candidate WP_012467218.1 CLIM_RS11700 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.25784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-124  401.7   0.0   3.3e-124  401.3   0.0    1.1  1  lcl|NCBI__GCF_000020465.1:WP_012467218.1  CLIM_RS11700 bifunctional aspart


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012467218.1  CLIM_RS11700 bifunctional aspartate kinase/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.3   0.0  3.3e-124  3.3e-124       5     441 ..       3     463 ..       1     464 [. 0.94

  Alignments for each domain:
  == domain 1  score: 401.3 bits;  conditional E-value: 3.3e-124
                                 TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekire 71 
                                               ++KFGG+S+g++ rikk+a i+ +  + +  +vVVvSA   vTd L+e a+ ++ ++e   +++++i +
  lcl|NCBI__GCF_000020465.1:WP_012467218.1   3 IYKFGGSSLGSAARIKKIAGIIRSGLQPD-CPVVVVSAFHRVTDLLLEAANVACTGREgyLRILDDIGQ 70 
                                               79************************888.999************************9998999***** PP

                                 TIGR00657  72 khlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaalee 127
                                                h + l+ l   +   + l++ +  el+e++             e++++l+ls+GE+lSa+++a++l+ 
  lcl|NCBI__GCF_000020465.1:WP_012467218.1  71 LHKTVLDGLFsGSDAYAGLSDSIRVELAELHDllhgvfllrelsEKSTALLLSFGERLSARIVAGYLNL 139
                                               **999999986666778888888888888888999********************************** PP

                                 TIGR00657 128 lgvkavsllgaeagiltdsefgrAkvleeikterl.eklleegiivvvaGFiGatekgeittLGRGGSD 195
                                               l    + +l+a++ i+td+++g+A+v  e++ +r+ ++ +  g+i+vv+G+i+a  +g +ttLGRGGSD
  lcl|NCBI__GCF_000020465.1:WP_012467218.1 140 LK-LPAVYLDARELIVTDANYGSATVDLEETFQRIvNAPVPDGVIPVVTGYIAAAGDGTTTTLGRGGSD 207
                                               **.5666889***************666666666505556677************************** PP

                                 TIGR00657 196 ltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrak 264
                                               +tA+l +aal+A+e+ i+tDVdG ++aDP+ v++Ar l+ isy+Ea+EL++ GakvLhp t+ pam+a+
  lcl|NCBI__GCF_000020465.1:WP_012467218.1 208 YTASLFGAALGAEEIFIWTDVDGFFSADPKRVRDARVLPFISYAEAMELSHAGAKVLHPFTILPAMKAS 276
                                               ********************************************************************* PP

                                 TIGR00657 265 ipivvkstfnpeaeGTlivaksk...seeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328
                                               ip+++k++fnp+a+GT i  + +   +++  +v++ls+ ++ +l+++sg++m   pgi++++f++la++
  lcl|NCBI__GCF_000020465.1:WP_012467218.1 277 IPVLIKNSFNPDAPGTRIERELDpvaVRQIHPVTGLSSINSVVLLNLSGSGMVgvPGIASRLFSCLAKH 345
                                               *********************9999988889************************************** PP

                                 TIGR00657 329 kvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapg 394
                                               ++nv+ i+q sse+sis++++  +a ka+++l+    ++++++ + ++ + ++lalv++vG++m+++pg
  lcl|NCBI__GCF_000020465.1:WP_012467218.1 346 HINVIFISQASSEQSISLAINPAQAAKANRILEdefAAEMQARLIDPLVLRRHLALVAVVGNNMSGHPG 414
                                               *******************************99777667888889999********************* PP

                                 TIGR00657 395 vaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               v a++fe+L +++in+ +++  ++e++isvv+d++d +ka++++he ++
  lcl|NCBI__GCF_000020465.1:WP_012467218.1 415 VSAQLFETLGKNGINVIAVAqgANEMNISVVIDNRDEDKALNCIHESFF 463
                                               ********************99************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (822 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 16.58
//
[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