Alignments for a candidate for asp-kinase in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methanococcus maripaludis C5

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011868345.1 MMARC5_RS02925 aspartate kinase

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000016125.1:WP_011868345.1
          Length = 468

 Score =  616 bits (1589), Expect = 0.0
 Identities = 314/471 (66%), Positives = 390/471 (82%), Gaps = 10/471 (2%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60
           M TVMKFGGTSVG+GERIR+VAKIV  +  ED DVVVV SAM++VTN+LVEIS QALDVR
Sbjct: 1   MVTVMKFGGTSVGNGERIRNVAKIVVNKTNEDKDVVVVTSAMTQVTNSLVEISAQALDVR 60

Query: 61  DIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPK 120
           DIAK+ +FI+ +R KH  AIE+AI++ +I+ EV K I S I +LEKVL+GV+YLGELTPK
Sbjct: 61  DIAKINNFIEDLRRKHEIAIEQAIENHDIRVEVSKTIQSSINDLEKVLVGVSYLGELTPK 120

Query: 121 SRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLLP 180
           S+D+ILSFGERLS+PILSGAIRD+G+ S+ L G +AGIITD+ F  A++ RL+V +++ P
Sbjct: 121 SKDFILSFGERLSAPILSGAIRDMGKHSLFLAGRDAGIITDDTFTCAKILRLDVADKIEP 180

Query: 181 LLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTDP 240
           LLK+G IPVVTGF+  TEEG+ITTLGRGGSDYSAAL+G GL A+++EIWTDVSGV + DP
Sbjct: 181 LLKDGFIPVVTGFVAGTEEGHITTLGRGGSDYSAALVGRGLMANMVEIWTDVSGVLSADP 240

Query: 241 RLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLITN 300
           R+V   ++IPK+SYIEAMELAYFGAKVLHPRT+EP MEK IP+ +KNTFEPE+EGTLIT+
Sbjct: 241 RMVENVKKIPKMSYIEAMELAYFGAKVLHPRTMEPVMEKKIPLRIKNTFEPENEGTLITD 300

Query: 301 DMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSETN 360
             E S+ ++KAI+TIK+V LINIFG GMVGVSGTAARIF  LG+   NVILI+QGSSETN
Sbjct: 301 SSETSNGVIKAITTIKDVILINIFGGGMVGVSGTAARIFNVLGKSNANVILITQGSSETN 360

Query: 361 ISLVV--SEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAK 418
           IS+V+   E +  K ++ L+ EFG+         +LI+D+S DKDVCV+SVVG+GM+GAK
Sbjct: 361 ISIVIYDGELEAKKCVRELRSEFGEC--------HLIKDISFDKDVCVVSVVGSGMKGAK 412

Query: 419 GIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIE 469
           GIAGK+F AV+ESGANIKMIAQGSSE NISFVI+E  L  C++ LH+ F+E
Sbjct: 413 GIAGKLFDAVAESGANIKMIAQGSSETNISFVINEDKLEPCLKNLHKTFVE 463


Lambda     K      H
   0.316    0.135    0.364 

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: 754
Number of extensions: 22
Number of successful extensions: 4
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: 473
Length of database: 468
Length adjustment: 33
Effective length of query: 440
Effective length of database: 435
Effective search space:   191400
Effective search space used:   191400
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: 51 (24.3 bits)

Align candidate WP_011868345.1 MMARC5_RS02925 (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.1229200.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-146  474.2  11.3   2.1e-146  474.0  11.3    1.0  1  NCBI__GCF_000016125.1:WP_011868345.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011868345.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.0  11.3  2.1e-146  2.1e-146       2     406 ..       1     463 [.       1     464 [. 0.93

  Alignments for each domain:
  == domain 1  score: 474.0 bits;  conditional E-value: 2.1e-146
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae..........llkll.... 60 
                                           +++V+KFGGtsvg++eri+++akiv+++++e+k+vvVV SAm +vt+ lve++           +        
  NCBI__GCF_000016125.1:WP_011868345.1   1 MVTVMKFGGTSVGNGERIRNVAKIVVNKTNEDKDVVVVTSAMTQVTNSLVEISAqaldvrdiakI---Nnfie 70 
                                           689*************************************************9888887775552...23334 PP

                             TIGR00656  61 ......eaisdei.......................................sprerdelvsvGEllssalls 88 
                                                 e     i                                       +p+++d ++s+GE+ls+++ls
  NCBI__GCF_000016125.1:WP_011868345.1  71 dlrrkhE-----IaieqaienhdirvevsktiqssindlekvlvgvsylgelTPKSKDFILSFGERLSAPILS 138
                                           4333330.....144555566667777788888888************************************* PP

                             TIGR00656  89 salrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeGeiTtLGRGGSD 161
                                           +a+r+ g+++  l g +agi+Tdd+f+ Aki +l+++ ++++lL++g i+vv+GF+  teeG+iTtLGRGGSD
  NCBI__GCF_000016125.1:WP_011868345.1 139 GAIRDMGKHSLFLAGRDAGIITDDTFTCAKILRLDVADKIEPLLKDGFIPVVTGFVAGTEEGHITTLGRGGSD 211
                                           ************************************************************************* PP

                             TIGR00656 162 ltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpil 234
                                           ++Aal++ +l A+ vei+TDV+Gv+++DPr+ve+ kki+k+sy Ea+elA++Gakvlhpr++e+ +e+k+p++
  NCBI__GCF_000016125.1:WP_011868345.1 212 YSAALVGRGLMANMVEIWTDVSGVLSADPRMVENVKKIPKMSYIEAMELAYFGAKVLHPRTMEPVMEKKIPLR 284
                                           ************************************************************************* PP

                             TIGR00656 235 vrsskeke.egTlitnkkens.slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtes 305
                                           +++++e+e egTlit+++e+s  ++kai++ k+v +++++g gm+g +g++a+if++L++++ nv+li+q++s
  NCBI__GCF_000016125.1:WP_011868345.1 285 IKNTFEPEnEGTLITDSSETSnGVIKAITTIKDVILINIFGGGMVGVSGTAARIFNVLGKSNANVILITQGSS 357
                                           ****************9999878************************************************** PP

                             TIGR00656 306 etsislvvdeed..vdeakkaLkeesgaae.lesleveedlavvsivgaglveapGvaseifkaleekninil 375
                                           et+is+v+ + +  +++ +++L++e+g+ + +++++ ++d++vvs+vg+g+++a+G+a+++f a++e+++ni+
  NCBI__GCF_000016125.1:WP_011868345.1 358 ETNISIVIYDGEleAKKCVRELRSEFGECHlIKDISFDKDVCVVSVVGSGMKGAKGIAGKLFDAVAESGANIK 430
                                           ********876511567889999999998899***************************************** PP

                             TIGR00656 376 mis..ssetkisvlvdekdaekavrklheklee 406
                                           mi+  sset+is++++e ++e + ++lh++++e
  NCBI__GCF_000016125.1:WP_011868345.1 431 MIAqgSSETNISFVINEDKLEPCLKNLHKTFVE 463
                                           *99889*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (468 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.49
//
[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