Alignments for a candidate for asp-kinase in Lacinutrix algicola AKS293

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Lacinutrix algicola AKS293

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_055435097.1 ASC41_RS02630 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_001418085.1:WP_055435097.1
          Length = 1131

 Score =  472 bits (1214), Expect = e-137
 Identities = 294/826 (35%), Positives = 480/826 (58%), Gaps = 42/826 (5%)

Query: 1    MKIIKFGGSSIANYENIQKVFSIIEQKSE-KEAFALVFSAFGGVTEQLLQCANIAQQSEE 59
            MKI+KFGG S+AN E + +V SIIE K + +E  A+V SA G  T+QL      A + +E
Sbjct: 327  MKILKFGGKSLANGEGLNRVISIIENKVKAEENIAVVVSARGKATDQLESILEKAVK-DE 385

Query: 60   SYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDY 119
            +Y T     +              Q+ T +   +  F  L  LF G+ L+ + S +  D 
Sbjct: 386  AYATDFDAFKN------------DQKGTIVVDFETEFLRLESLFAGVQLLGDYSPKIKDE 433

Query: 120  VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179
            VL+ GE +S  ++   L  K I     DAR  +KTDD FG+AK     + K +  +FK +
Sbjct: 434  VLAQGELISAKLITGLLVDKNINAKVADARTFIKTDDTFGNAKPIDALSKKNVVAYFKQN 493

Query: 180  DD--IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRL 237
            +   + ++TGFI S    +TTT+GR+GS+YTA++ A  L AE+++ +T V+G+ TA+P L
Sbjct: 494  NGTTVNIVTGFIASNRDNKTTTLGRNGSNYTAALLANYLDAEELQNYTHVNGIYTANPDL 553

Query: 238  VYTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS 297
            V  A  I +LS+ EA EL++FG  ++   T+ P ++++IP+ I NTF P++ GT I+  +
Sbjct: 554  VADAIKIERLSFTEANELANFGTTILHAKTIIPLIEKNIPLRILNTFNPEDKGTIITAQN 613

Query: 298  GEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICV 357
             + K I+ +S +DN++++N++G GL+  VGV  R F  L+   I++ +ISQ SSE  I +
Sbjct: 614  -KDKGIRSLSVLDNVALVNIEGRGLLGKVGVDARIFTALSKENISVSIISQGSSERGIGL 672

Query: 358  AIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQ--HNPGASGRMFQ 415
             I ++ A+RA  V+E+EF  +  S ++++I ++ D++VI+++G+ +   H P      F 
Sbjct: 673  VIEAEHANRAVIVLEQEFENDFYSQDINKISVIDDVSVISIIGQELSTFHKP------FN 726

Query: 416  ALGRNNVNVAAIAQGSSELNISAVITQADLQKALNALH-EAFFLSDYKVLHLFLVGVGLI 474
             L +N +         +  N+S V+ + +L KA+N +H E F +S  K ++L + G GL+
Sbjct: 727  NLIKNQIIPILFNNTITGENVSIVVKKKELHKAVNVIHGEIFGIS--KKINLAIFGHGLV 784

Query: 475  GKALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDK 534
            G AL   I    K++++   + + I  +ANS+   F ++G D       + N E   ++ 
Sbjct: 785  GGALVNQIIASAKDIEKRKGIKLNIFAIANSQKALFSKNGIDENWKNTLETNGENYKIED 844

Query: 535  FIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLA 594
                  + +  N + +D T+S +    Y ++++    +V+ NK AN+  LE Y +L+   
Sbjct: 845  VFQFAKDNHLENLIAIDNTSSLEFVSNYIKLVEQGFDLVSSNKIANTIDLEFYNELRNTL 904

Query: 595  GQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSEL-EKGMPFSE 653
             +    + YETNV AGLP+I+T++ L LSG+++ RI  V SGS++Y+F+    +   F+ 
Sbjct: 905  EKHQKSYLYETNVGAGLPLIDTIKLLHLSGENIVRIRGVFSGSLSYLFNTFSSEDTSFAT 964

Query: 654  VVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFE--DVEIQSMVPEDCEDAA 711
            V+ QA +KG+TEP+PR+DLSG DVARK+LIL RE   DLH E  DV I++++PE   +  
Sbjct: 965  VLQQALDKGFTEPNPREDLSGNDVARKLLILAREL--DLHNEIGDVTIENLIPEPLRE-I 1021

Query: 712  SVPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATL------ENG-KAKVGLNSLDSEHP 764
               +F   L + +  FQ+ + EA  +G  LR++  L      ENG +  V L S+ S+ P
Sbjct: 1022 ETSQFLDSLDEMNTVFQK-IKEAQKEGHVLRYIGDLHGDLSQENGAQLDVKLESVPSQSP 1080

Query: 765  FFTLKGSDNMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRL 810
               L+G+D++    TE Y + P++++G GAGA VTA GVF DI+RL
Sbjct: 1081 LGALQGADSIFEIYTESYGEKPIVIQGAGAGASVTARGVFGDILRL 1126


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: 2042
Number of extensions: 96
Number of successful extensions: 12
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: 1131
Length adjustment: 44
Effective length of query: 771
Effective length of database: 1087
Effective search space:   838077
Effective search space used:   838077
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: 57 (26.6 bits)

Align candidate WP_055435097.1 ASC41_RS02630 (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.163069.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.9e-96  308.7   9.0    6.3e-96  308.0   9.0    1.3  1  NCBI__GCF_001418085.1:WP_055435097.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055435097.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.0   9.0   6.3e-96   6.3e-96       5     440 ..     329     767 ..     326     769 .. 0.88

  Alignments for each domain:
  == domain 1  score: 308.0 bits;  conditional E-value: 6.3e-96
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlea 76 
                                           ++KFGG S++n+e +++v  i++++ + +++ +VVvSA+++ Td+L ++ ek+ ++e  ++  ++ ++++   
  NCBI__GCF_001418085.1:WP_055435097.1 329 ILKFGGKSLANGEGLNRVISIIENKVKAEENIAVVVSARGKATDQLESILEKAVKDEAyATDFDAFKNDQ--- 398
                                           79**************************************************999995322233332222... PP

                             TIGR00657  77 leelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsllg 137
                                                    k +++ + e+e+  +++            ++ +d++l+ GE +Sa+l++++l +++  ++++ +
  NCBI__GCF_001418085.1:WP_055435097.1 399 ---------KGTIVVDFETEFLRLESlfagvqllgdysPKIKDEVLAQGELISAKLITGLLVDKN-INAKVAD 461
                                           .........22333333333333333444445566677***************************.889**** PP

                             TIGR00657 138 aeagiltdsefgrAkvleeikterleklleeg...iivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                           a+  i td++fg+Ak +   +++++ ++ +++   ++ +v+GFi++++++++ttLGR+GS +tAallA+ l+A
  NCBI__GCF_001418085.1:WP_055435097.1 462 ARTFIKTDDTFGNAKPIDALSKKNVVAYFKQNngtTVNIVTGFIASNRDNKTTTLGRNGSNYTAALLANYLDA 534
                                           ***************777777777777666655899************************************* PP

                             TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGT 280
                                           +e++ yt V+Giyta P +v +A +++ +s+ Ea ELa++G  +Lh +t+ p+++++ip+++ +tfnpe +GT
  NCBI__GCF_001418085.1:WP_055435097.1 535 EELQNYTHVNGIYTANPDLVADAIKIERLSFTEANELANFGTTILHAKTIIPLIEKNIPLRILNTFNPEDKGT 607
                                           ************************************************************************* PP

                             TIGR00657 281 livakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351
                                           +i+a++k   ++ +++ls+ +n alv+++g +    +g+ a++f+al++++++v +i+q sse +i +v++ e
  NCBI__GCF_001418085.1:WP_055435097.1 608 IITAQNK---DKGIRSLSVLDNVALVNIEGRGLLgkVGVDARIFTALSKENISVSIISQGSSERGIGLVIEAE 677
                                           *****77...467*******************9999************************************* PP

                             TIGR00657 352 dadkakellkkkvkee...kaleevevekklalvslvGagmksapgvaakifeaLaeen.iniemis.sseik 419
                                           +a++a+ +l+++++++   +++++++v ++++++s++G+++++      k f++L +++ i+i      +  +
  NCBI__GCF_001418085.1:WP_055435097.1 678 HANRAVIVLEQEFENDfysQDINKISVIDDVSVISIIGQELST----FHKPFNNLIKNQiIPILFNNtITGEN 746
                                           **********888885333789999****************99....6677777777661566665588899* PP

                             TIGR00657 420 isvvvdekdaekavealhekl 440
                                           +s+vv++k+ +kav+++h ++
  NCBI__GCF_001418085.1:WP_055435097.1 747 VSIVVKKKELHKAVNVIHGEI 767
                                           ******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (1131 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: 54.81
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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