Alignments for a candidate for asp-kinase in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pedobacter sp. GW460-11-11-14-LB5

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate CA265_RS09655 CA265_RS09655 aspartate kinase

Query= BRENDA::Q9S702
         (559 letters)



>FitnessBrowser__Pedo557:CA265_RS09655
          Length = 437

 Score =  233 bits (593), Expect = 1e-65
 Identities = 170/470 (36%), Positives = 257/470 (54%), Gaps = 50/470 (10%)

Query: 86  VMKFGGSSVASAERMIQVAKLILSFPDEKPVVVLSAMAKTTNKLL------MAGEK---A 136
           ++KFGG+SV S ERM ++  +I   P+E+ +VVLSA++ TTN L+      +AG+K   +
Sbjct: 3   ILKFGGTSVGSPERMTKLLDIIN--PNEEQIVVLSAVSGTTNSLVEIANYFLAGDKKKGS 60

Query: 137 VCCGVTNVDTIEELSYIKELHIRTAHELGVETAVIAEHLEGLEQLLKGVAMMKELTLRSR 196
            C  V N+    +   ++ L      E G E  VI  H   L  L   +      T    
Sbjct: 61  EC--VENLYQKYKTFVVELLPAAEFQEQGNE--VIDYHFGFLAGLANDI-----FTSIEE 111

Query: 197 DYLVSFGECMSTRLFAAYLNKIGHKARQYDAFEIGIITTDDFTNADILEATYPAVSKKL- 255
             +++ GE +ST L+  YL  IG  +    A +   + TD+    DI     P  +K L 
Sbjct: 112 KVVLAQGELLSTTLYHIYLKSIGVPSVLLPALDF--MKTDEDNEPDI-----PFTTKHLT 164

Query: 256 -LGDWSKENALPVVTGFLGKGWRSCAVTTLGRGGSDLTATTIGKALGLREIQVWKDVDGV 314
            L +  K+N L +  G++ +      V  L RGGSD TA+ +G A+   E+Q+W D+DG+
Sbjct: 165 PLLEQHKDNKLFITQGYICRNSFG-EVDNLRRGGSDYTASLLGAAILAEEVQIWTDIDGM 223

Query: 315 LTCDPNIYCGAQPVPHLTFDEAAELAYFGAQVLHPLSMRPAREGNIPVRVKNSYNPTAPG 374
              DP I  G +P+  L+FDEAAELAYFGA++LHP S+ PA++  IPVR+ N+  P+A G
Sbjct: 224 HNNDPRIVKGTKPIAQLSFDEAAELAYFGAKILHPQSVFPAQKYKIPVRLLNTMEPSAAG 283

Query: 375 TVITRSRDMSKAVLTSIVLKRNVTMLDITSTRMLGQYGFLAKVFSTFEKLGISVDVVATS 434
           T+IT   D  +  + SI  K  +T + I S+RML  YGFL +VF  FE+    +D++ TS
Sbjct: 284 TLIT--HDSERGKIKSIAAKDGITAIRIQSSRMLLAYGFLRRVFEVFERYKTPIDMITTS 341

Query: 435 EVSISLTLDPSKFCSRELIQHELDQVVEELEKIAVVNLLRHRSIISLIGNVQRSSFILEK 494
           EV++SLT+D +           L Q++EELE    V +  + SI+ ++G+     F  EK
Sbjct: 342 EVAVSLTIDETA---------HLPQIIEELESFGTVEVDTNHSIVCVVGD-----FGSEK 387

Query: 495 -GF--RVLR-TNGINVQMISQGASKVNISLIVNDDEAEHCVKALHSAFFE 540
            GF  RVL     I ++MIS G S  N+SL++  +     +++LH+  FE
Sbjct: 388 HGFASRVLEGLKHIPIRMISYGGSNYNVSLLILSEYKTEALRSLHNRLFE 437


Lambda     K      H
   0.319    0.133    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: 475
Number of extensions: 21
Number of successful extensions: 7
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: 559
Length of database: 437
Length adjustment: 34
Effective length of query: 525
Effective length of database: 403
Effective search space:   211575
Effective search space used:   211575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate CA265_RS09655 CA265_RS09655 (aspartate kinase)
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.20063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    6.9e-90  288.1   0.0    7.9e-90  287.9   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS09655  CA265_RS09655 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS09655  CA265_RS09655 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.9   0.0   7.9e-90   7.9e-90       5     442 .]       3     437 .]       1     437 [] 0.87

  Alignments for each domain:
  == domain 1  score: 287.9 bits;  conditional E-value: 7.9e-90
                                  TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...kelieki 69 
                                                ++KFGGtSvg+ er+ k+ +i+  ++    + +VV+SA++g+T++Lve+a+ +  +++    e +e++
  lcl|FitnessBrowser__Pedo557:CA265_RS09655   3 ILKFGGTSVGSPERMTKLLDIINPNE----EQIVVLSAVSGTTNSLVEIANYFLAGDKkkgSECVENL 66 
                                                79********************9887....779********************999965555555555 PP

                                  TIGR00657  70 rekhlealeela.sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelg 129
                                                 +k  + + el    + +e+ ++++++++  +         + e+ ++l+ GE lS++l   +l++ g
  lcl|FitnessBrowser__Pedo557:CA265_RS09655  67 YQKYKTFVVELLpAAEFQEQGNEVIDYHFGFLAGlandiftSIEEKVVLAQGELLSTTLYHIYLKSIG 134
                                                55555555555545555666666666665555549999*99999************************ PP

                                  TIGR00657 130 vkavsllgaeagiltdsefgrAkvleeikterleklleeg...iivvvaGFiGatekgeittLGRGGS 194
                                                v +v l  a   + td+  +        +t+ l++lle+    ++ +++G+i  ++ ge+  L RGGS
  lcl|FitnessBrowser__Pedo557:CA265_RS09655 135 VPSVLL-PALDFMKTDEDNEPDI---PFTTKHLTPLLEQHkdnKLFITQGYICRNSFGEVDNLRRGGS 198
                                                777755.5555666776554444...455555555555433448************************ PP

                                  TIGR00657 195 DltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamr 262
                                                D+tA+ll+aa+ A+ev+i+tD+dG +  DPriv+ ++ ++++s++Ea+ELa++Gak+Lhp+++ pa +
  lcl|FitnessBrowser__Pedo557:CA265_RS09655 199 DYTASLLGAAILAEEVQIWTDIDGMHNNDPRIVKGTKPIAQLSFDEAAELAYFGAKILHPQSVFPAQK 266
                                                ******************************************************************** PP

                                  TIGR00657 263 akipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328
                                                +kip++  +t++p+a GTli+ +s+   + ++k+++ ++  + + ++++ m   +g+l +vf+  ++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS09655 267 YKIPVRLLNTMEPSAAGTLITHDSE---RGKIKSIAAKDGITAIRIQSSRMLlaYGFLRRVFEVFERY 331
                                                ***********************55...568********************999************** PP

                                  TIGR00657 329 kvnvdlilqsssetsisfvvdked.adkakellkkkvkeekaleevevekklalvslvGagmksapgv 395
                                                k  +d+i+  +se  +s+++d++  ++++ e+       ++ +++vev+++ ++v +vG+  +++ g 
  lcl|FitnessBrowser__Pedo557:CA265_RS09655 332 KTPIDMIT--TSEVAVSLTIDETAhLPQIIEE-------LESFGTVEVDTNHSIVCVVGDFGSEKHGF 390
                                                ********..8888899999987656666665.......578************************** PP

                                  TIGR00657 396 aakifeaLaeeniniemis..sseikisvvvdekdaekavealheklve 442
                                                a++++e L++  i+i+mis   s++++s+++ +++ ++a++ lh++l+e
  lcl|FitnessBrowser__Pedo557:CA265_RS09655 391 ASRVLEGLKH--IPIRMISygGSNYNVSLLILSEYKTEALRSLHNRLFE 437
                                                *********9..********99************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (437 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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