Alignments for a candidate for asp-kinase in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Halomonas desiderata SP1

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_086509286.1 BZY95_RS07285 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_002151265.1:WP_086509286.1
          Length = 416

 Score =  563 bits (1452), Expect = e-165
 Identities = 296/409 (72%), Positives = 348/409 (85%), Gaps = 5/409 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           MAL VQKFGGTSVG+VERI+ VAEKVK FRD G  +VVVVSAMSGETNRLI +A +I+++
Sbjct: 1   MALYVQKFGGTSVGSVERIKAVAEKVKGFRDDGHQVVVVVSAMSGETNRLIAMANEINDE 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
           P PRE+D++VSTGEQVTI+LLA+AL K GVPA SYTG+QV ILTDSAHTKARI +I+   
Sbjct: 61  PTPREMDMLVSTGEQVTISLLALALHKLGVPATSYTGSQVGILTDSAHTKARIQRIETDE 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           ++ D+  G+VVVVAGFQGVDE+GNITTLGRGGSDTTGVALAAAL ADECQIYTDVDGVYT
Sbjct: 121 MREDLDEGKVVVVAGFQGVDEEGNITTLGRGGSDTTGVALAAALGADECQIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240
           TDPRV +KAQRLD IT EEMLE+ASLGSKVLQIR+VEFAGKY+VPLRVL SFQ+GPGTLI
Sbjct: 181 TDPRVCSKAQRLDTITVEEMLELASLGSKVLQIRSVEFAGKYNVPLRVLSSFQDGPGTLI 240

Query: 241 TLD---EEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQN 297
             +   +E+SME+P+ISGIAF  +EAKLT+   PD PGVA +ILGPI+ AN+EVDMIVQN
Sbjct: 241 VAESDQDEDSMEEPLISGIAFTANEAKLTLLHTPDVPGVASRILGPIADANIEVDMIVQN 300

Query: 298 VA-HDNTTDFTFTVHRNDYNNALQVL-QGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAG 355
           VA   + TDFTFTV + DY   L++L + +  ++G  E  GD NIAKVS+VGVGMRSHAG
Sbjct: 301 VAPAGDYTDFTFTVAKGDYKKTLKILEEQVIPDLGGGEVNGDDNIAKVSLVGVGMRSHAG 360

Query: 356 VASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
           VA++MF  LA ENINI+M+STSEIK+SVVI+EK +ELAVRALHTAF LD
Sbjct: 361 VAAKMFRVLADENINIRMVSTSEIKISVVIDEKQMELAVRALHTAFGLD 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: 600
Number of extensions: 17
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: 416
Length adjustment: 31
Effective length of query: 381
Effective length of database: 385
Effective search space:   146685
Effective search space used:   146685
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_086509286.1 BZY95_RS07285 (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.1066951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-139  451.0   9.7   2.3e-139  450.8   9.7    1.0  1  NCBI__GCF_002151265.1:WP_086509286.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002151265.1:WP_086509286.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.8   9.7  2.3e-139  2.3e-139       2     405 ..       2     407 ..       1     409 [. 0.97

  Alignments for each domain:
  == domain 1  score: 450.8 bits;  conditional E-value: 2.3e-139
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 
                                            l VqKFGGtsvgs+erik++a++v+    +g++vvVVvSAms++t++l+++a      + i+de++pre+d+
  NCBI__GCF_002151265.1:WP_086509286.1   2 ALYVQKFGGTSVGSVERIKAVAEKVKGFRDDGHQVVVVVSAMSGETNRLIAMA------NEINDEPTPREMDM 68 
                                           688**************************************************......8************* PP

                             TIGR00656  75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147
                                           lvs+GE+++++ll+ al++lgv a++++g + gilTd+ +++A+i++++t  ++ e L+eg++vvvaGF+G +
  NCBI__GCF_002151265.1:WP_086509286.1  69 LVSTGEQVTISLLALALHKLGVPATSYTGSQVGILTDSAHTKARIQRIET-DEMREDLDEGKVVVVAGFQGVD 140
                                           **************************************************.9********************* PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                           eeG+iTtLGRGGSD+t ++laaal Ad+++iyTDV+GvyttDPrv ++a+++d+i++eE+lelA+lG kvl+ 
  NCBI__GCF_002151265.1:WP_086509286.1 141 EEGNITTLGRGGSDTTGVALAAALGADECQIYTDVDGVYTTDPRVCSKAQRLDTITVEEMLELASLGSKVLQI 213
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskekeegTlitn.......kkensslvkaialeknvarltvegegmlgkrgilaei 286
                                           r++e+a +++vp++v ss++   gTli++       ++e++ l+++ia++ n a+lt+   +  + +g++++i
  NCBI__GCF_002151265.1:WP_086509286.1 214 RSVEFAGKYNVPLRVLSSFQDGPGTLIVAesdqdedSMEEP-LISGIAFTANEAKLTLL--HTPDVPGVASRI 283
                                           ****************************9888887667777.****************9..99********** PP

                             TIGR00656 287 fkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesg.aaelesleveedlavvsivgaglv 354
                                            + +a+++i vd+i+q  +     t+ +++v++ d +++ k+L+e+++ +++  +++ + ++a+vs+vg+g++
  NCBI__GCF_002151265.1:WP_086509286.1 284 LGPIADANIEVDMIVQNVAPagdyTDFTFTVAKGDYKKTLKILEEQVIpDLGGGEVNGDDNIAKVSLVGVGMR 356
                                           ****************98767789********************9986355689******************* PP

                             TIGR00656 355 eapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           ++ Gva+++f +l+++nini m+s+se+kisv++dek++e avr+lh ++ 
  NCBI__GCF_002151265.1:WP_086509286.1 357 SHAGVAAKMFRVLADENINIRMVSTSEIKISVVIDEKQMELAVRALHTAFG 407
                                           ***********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (416 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: 26.37
//
[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 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