Alignments for a candidate for asp-kinase in Aquimarina longa SW024

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Aquimarina longa SW024

Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_062056268.1 N456_RS09495 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Pedo557:CA265_RS23475
         (817 letters)



>NCBI__GCF_001401755.1:WP_062056268.1
          Length = 804

 Score =  485 bits (1249), Expect = e-141
 Identities = 292/822 (35%), Positives = 469/822 (57%), Gaps = 32/822 (3%)

Query: 1   MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSP--VVVLSAMSGVTNLLTEMAEMAERGE 58
           MKVLKFGG S+ + + I T++ ++ E+K KN     VVLSA    TN L E+ E A + +
Sbjct: 1   MKVLKFGGKSLANGKGIHTVIDII-EDKVKNGEKITVVLSARGNTTNELEEILEKAVKNQ 59

Query: 59  DYDTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQ 118
            Y         K F   +    A   +  F+R    F  L+ L + V+ L + S + KDQ
Sbjct: 60  SYQ--------KEFESFKEYQKADFLDIDFSRE---FETLDKLFEGVSLLGDYSKRIKDQ 108

Query: 119 ILSYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELT-EMLINNFYQE 177
           +LS GE  S  +++ I      ++ + +  DLI TD  FG A+   +L+ E +IN+F + 
Sbjct: 109 VLSQGEVVSAKLVTQILKGKNINAKFTDSRDLIITDDQFGDAQPLDKLSKENVINHFQEY 168

Query: 178 NKDKVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRM 237
           N   V  VTGFIASN     TTLGR GS+YTA++    L AEE++ +T VNG+ TA+P +
Sbjct: 169 NGTTVNIVTGFIASNTKNETTTLGRNGSNYTASLLANYLEAEELQNFTHVNGIYTANPDL 228

Query: 238 VKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDV 297
           V  A  + +LS+TEA EL+YFGA +++  T+IP   K IP+ I NTF     GT I ++ 
Sbjct: 229 VPDAQKIEKLSFTEANELAYFGANILHAKTIIPLIEKNIPLRILNTFNYKNKGTLITAE- 287

Query: 298 KASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSIT 357
            AS   IK +S ++H+++INL G G++GK G   R+F  L+ + I+V +I+Q SSE  I 
Sbjct: 288 -ASEKGIKSLSVLEHVALINLEGRGLLGKVGVDARIFRALAHKNISVSIISQGSSERGIG 346

Query: 358 FAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNA 417
           F V+   A +A S++++EFE +   + +    +E N++V++I+G+++        + +NA
Sbjct: 347 FVVEADKAKEAKSVLEQEFESDFYKRDVSGITIEENVSVISIIGQDL----STFHKPYNA 402

Query: 418 LGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGK 477
           L +N +         +  N+S+++ K+ L +A+N +H   F ++ + +NV   G G +G 
Sbjct: 403 LIKNQVIPLLFNNTVTGKNVSLVVRKEQLHRALNVIHGEIF-EIAKKINVAIFGHGLVGG 461

Query: 478 TLFNQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGF 537
           TL NQ+ +    +     + + +  ++N++K++F   G+  +NWE+E+  +G    +   
Sbjct: 462 TLINQILKSSNQIEKRKKIAINIFAVANSKKVLFDQTGID-QNWESEIVEHGVSYTIDDI 520

Query: 538 VAKMKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTAR 597
           +      +L N + +DNTA++   + Y  +      +V+ NK  N+  +  YK  +    
Sbjct: 521 IQFADKHHLENLIAIDNTASQDFTKHYIHLVAHGFDLVSSNKVANTLSFDFYKELRVKLE 580

Query: 598 KFGVDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAG-FYET 656
           +    + YETNVGAGLP+I T++ L +SG+ + RI+ + SG++SY+FN F  E   F E 
Sbjct: 581 ENQKQYLYETNVGAGLPLIDTIKLLHLSGENITRIKGVFSGSLSYLFNTFSIEKRLFSEV 640

Query: 657 VKEAQELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVE 716
           ++EA + G+TEPDPR+DL G D  RK+LILAR+     E  D+KI N++PE  L A   +
Sbjct: 641 LQEAIDNGFTEPDPREDLCGNDVGRKLLILARELDLSNEFDDIKIHNLIPEE-LRAGEAK 699

Query: 717 DFYSELQANAAYFENLKQTAANDGKVLRYIGKL------EDGNVEISLQMVDDSHPFYML 770
           +F   L+   + ++ +K+    D  VLRYIG L      E GN+++ L  V  S     +
Sbjct: 700 EFLGRLKELDSVYQKIKEEQKPD-HVLRYIGDLWGDLSQEKGNLDVKLVSVPQSSALGQV 758

Query: 771 SGSDNIISFTTDRYKSRPLVVKGPGAGAEVTAAGVFADIINV 812
            GSD+I    T+ Y  +P+V++G GAGA VTA GVF DI+ +
Sbjct: 759 KGSDSIFEIYTESYGDQPIVIQGAGAGAAVTARGVFGDILRL 800


Lambda     K      H
   0.316    0.133    0.369 

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: 1532
Number of extensions: 97
Number of successful extensions: 11
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: 817
Length of database: 804
Length adjustment: 41
Effective length of query: 776
Effective length of database: 763
Effective search space:   592088
Effective search space used:   592088
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 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate WP_062056268.1 N456_RS09495 (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.3153245.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-100  322.5   5.2   4.2e-100  321.8   5.2    1.3  1  NCBI__GCF_001401755.1:WP_062056268.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001401755.1:WP_062056268.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.8   5.2  4.2e-100  4.2e-100       5     441 ..       3     443 ..       1     444 [. 0.88

  Alignments for each domain:
  == domain 1  score: 321.8 bits;  conditional E-value: 4.2e-100
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekirekhleal 77 
                                           V+KFGG S++n++ i+ v +i++ + ++g++  VV+SA++++T++L e+ ek+ ++++        +k++e  
  NCBI__GCF_001401755.1:WP_062056268.1   3 VLKFGGKSLANGKGIHTVIDIIEDKVKNGEKITVVLSARGNTTNELEEILEKAVKNQS-------YQKEFESF 68 
                                           89*******************************************************6.......34555555 PP

                             TIGR00657  78 eela.sqalkeklkallekeleevkk........ereldlilsvGEklSaallaaaleelgvkavsllgaeag 141
                                           +e +  ++l   +++  e+  ++ +         +r +d +ls GE +Sa+l++++l+ ++  ++++++++  
  NCBI__GCF_001401755.1:WP_062056268.1  69 KEYQkADFLDIDFSREFETLDKLFEGvsllgdysKRIKDQVLSQGEVVSAKLVTQILKGKN-INAKFTDSRDL 140
                                           5555444444444444444444443367788889***************************.899******** PP

                             TIGR00657 142 iltdsefgrAkvleeikterleklleeg...iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeve 211
                                           i+td++fg+A+ l + ++e++ ++ +e    ++ +v+GFi+++ k+e+ttLGR+GS +tA+llA+ l+A+e++
  NCBI__GCF_001401755.1:WP_062056268.1 141 IITDDQFGDAQPLDKLSKENVINHFQEYngtTVNIVTGFIASNTKNETTTLGRNGSNYTASLLANYLEAEELQ 213
                                           ***********666666665555554433789***************************************** PP

                             TIGR00657 212 iytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTliva 284
                                            +t V+Giyta P +vp+A++++++s+ Ea ELa++Ga +Lh +t+ p+++++ip+++ +tfn +++GTli+a
  NCBI__GCF_001401755.1:WP_062056268.1 214 NFTHVNGIYTANPDLVPDAQKIEKLSFTEANELAYFGANILHAKTIIPLIEKNIPLRILNTFNYKNKGTLITA 286
                                           ************************************************************************* PP

                             TIGR00657 285 kskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadk 355
                                           + +   e+ +k+ls+ ++ al++++g +    +g+ a++f+ala+++++v +i+q sse +i fvv+ ++a++
  NCBI__GCF_001401755.1:WP_062056268.1 287 EAS---EKGIKSLSVLEHVALINLEGRGLLgkVGVDARIFRALAHKNISVSIISQGSSERGIGFVVEADKAKE 356
                                           *55...478*******************9999***************************************** PP

                             TIGR00657 356 akellkkkvke...ekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvv 423
                                           ak++l++++++   +++++ +++e++++++s++G+++++      k  +aL ++++    +    +  ++s+v
  NCBI__GCF_001401755.1:WP_062056268.1 357 AKSVLEQEFESdfyKRDVSGITIEENVSVISIIGQDLST----FHKPYNALIKNQVIPLLFNntVTGKNVSLV 425
                                           *****9766652226788899*****************9....6666777777665444444578899***** PP

                             TIGR00657 424 vdekdaekavealheklv 441
                                           v++++ ++a++++h +++
  NCBI__GCF_001401755.1:WP_062056268.1 426 VRKEQLHRALNVIHGEIF 443
                                           **************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (804 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: 00:00:00.00
# Mc/sec: 45.04
//
[ok]

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