Alignments for a candidate for asp-kinase in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Rhodospirillum centenum SW SW; ATCC 51521

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012567802.1 RC1_RS12695 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_000016185.1:WP_012567802.1
          Length = 411

 Score =  451 bits (1160), Expect = e-131
 Identities = 238/409 (58%), Positives = 307/409 (75%), Gaps = 5/409 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           MA +V KFGGTSVG +ERI  VA KVK+  D G ++ VVVSAMSG TN+L++  + IS  
Sbjct: 1   MARLVLKFGGTSVGDIERIRNVARKVKQEVDAGHEVAVVVSAMSGVTNQLVEYCRSISRI 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
              RE D +V++GEQVT  LLA+AL   G+ A S+ G Q+ ILTD  H KARI +ID   
Sbjct: 61  YDAREYDAVVASGEQVTSGLLAIALQDLGITARSWQGWQIPILTDDVHAKARIERIDTTE 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           I R +K G V VVAGFQGV  +  I+TLGRGGSDT+ VALAAAL A+ C IYTDVDGVYT
Sbjct: 121 IDRRMKTGEVAVVAGFQGVSHRNRISTLGRGGSDTSAVALAAALGAERCDIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGT-- 238
           TDPR+VAKA++L +IT+EEMLEMASLG+KVLQ R+VE A K+ V ++VL +F+E PG+  
Sbjct: 181 TDPRIVAKARKLSRITYEEMLEMASLGAKVLQTRSVEMAMKHRVRVQVLSTFEEAPGSDL 240

Query: 239 --LITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQ 296
              + +DE+E +EQ ++SGIA++RDEAK+T+ GV D PGVA +I GP++ A + VDMIVQ
Sbjct: 241 PGTLVVDEDEIVEQELVSGIAYSRDEAKVTLVGVADRPGVAARIFGPLADAAINVDMIVQ 300

Query: 297 NVAHD-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAG 355
           NV+ D  TTD TFTV + D + A+QVL+    E+  R  + D+++ K+S++GVGMRSHAG
Sbjct: 301 NVSEDGTTTDMTFTVGKADLDRAVQVLEKAKDELSYRRIVADSDVVKISVIGVGMRSHAG 360

Query: 356 VASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
           VA RMF+ALA   INIQ+ISTSEIKVSV++ E+Y ELA+RALHT + LD
Sbjct: 361 VAQRMFKALADRGINIQVISTSEIKVSVLVAEEYTELALRALHTVYGLD 409


Lambda     K      H
   0.317    0.133    0.357 

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: 463
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: 412
Length of database: 411
Length adjustment: 31
Effective length of query: 381
Effective length of database: 380
Effective search space:   144780
Effective search space used:   144780
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: 50 (23.9 bits)

Align candidate WP_012567802.1 RC1_RS12695 (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.231345.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-132  427.3  15.0   3.5e-132  427.2  15.0    1.0  1  NCBI__GCF_000016185.1:WP_012567802.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016185.1:WP_012567802.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.2  15.0  3.5e-132  3.5e-132       4     405 ..       4     407 ..       1     409 [. 0.96

  Alignments for each domain:
  == domain 1  score: 427.2 bits;  conditional E-value: 3.5e-132
                             TIGR00656   4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelv 76 
                                            V KFGGtsvg++eri+++a++v++e+  g++v VVvSAms+vt++lve        ++is     re d +v
  NCBI__GCF_000016185.1:WP_012567802.1   4 LVLKFGGTSVGDIERIRNVARKVKQEVDAGHEVAVVVSAMSGVTNQLVEYC------RSISRIYDAREYDAVV 70 
                                           699************************************************......79999999******** PP

                             TIGR00656  77 svGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGatee 149
                                           + GE+++s ll+ al++lg  a++ +g++ +ilTdd + +A+i++++t  ++  +++ g + vvaGF+G  + 
  NCBI__GCF_000016185.1:WP_012567802.1  71 ASGEQVTSGLLAIALQDLGITARSWQGWQIPILTDDVHAKARIERIDT-TEIDRRMKTGEVAVVAGFQGVSHR 142
                                           ************************************************.************************ PP

                             TIGR00656 150 GeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpra 222
                                            +i tLGRGGSD++A++laaal A+r++iyTDV+GvyttDPr+v +a+k+ +i+yeE+le+A+lGakvl+ r+
  NCBI__GCF_000016185.1:WP_012567802.1 143 NRISTLGRGGSDTSAVALAAALGAERCDIYTDVDGVYTTDPRIVAKARKLSRITYEEMLEMASLGAKVLQTRS 215
                                           ************************************************************************* PP

                             TIGR00656 223 lelaveakvpilvrsskek....e.egTlitn..kkensslvkaialeknvarltvegegmlgkrgilaeifk 288
                                           +e+a++  v + v s++e+    +  gTl+++  +  +++lv++ia++++ a++t++  g+++++g++a+if+
  NCBI__GCF_000016185.1:WP_012567802.1 216 VEMAMKHRVRVQVLSTFEEapgsDlPGTLVVDedEIVEQELVSGIAYSRDEAKVTLV--GVADRPGVAARIFG 286
                                           ****************997333235689999955444558*****************..9************* PP

                             TIGR00656 289 aLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveap 357
                                            La++ invd+i+q  se    t+++++v + d+d+a+++L++ ++++ ++++  ++d+ ++s++g+g++++ 
  NCBI__GCF_000016185.1:WP_012567802.1 287 PLADAAINVDMIVQNVSEdgttTDMTFTVGKADLDRAVQVLEKAKDELSYRRIVADSDVVKISVIGVGMRSHA 359
                                           *****************99*999************************************************** PP

                             TIGR00656 358 Gvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           Gva+++fkal++++ini  is+se+k+svlv e+++e a r+lh ++ 
  NCBI__GCF_000016185.1:WP_012567802.1 360 GVAQRMFKALADRGINIQVISTSEIKVSVLVAEEYTELALRALHTVYG 407
                                           ********************************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (411 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.35
//
[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