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_RS06275 CA265_RS06275 aspartate kinase

Query= BRENDA::Q57991
         (473 letters)



>FitnessBrowser__Pedo557:CA265_RS06275
          Length = 422

 Score =  184 bits (466), Expect = 6e-51
 Identities = 132/421 (31%), Positives = 214/421 (50%), Gaps = 40/421 (9%)

Query: 4   VMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIA 63
           + KFGG SV   + +++VA IV   KK   ++++V+SAM +VT+ L +++Q  L   + A
Sbjct: 3   IFKFGGASVKDADGVKNVANIVRDYKK--GNLLIVISAMGKVTDKLEKLTQAFLSQNNEA 60

Query: 64  KVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSR- 122
                   I+  H+  I+E  + +          +   +++    + + +L E  P +  
Sbjct: 61  HA--IFDEIKHFHFNIIDELFQGKA---------NPVYDDVANTFVEIDWLIEDEPDNNE 109

Query: 123 ----DYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLE----V 174
               D I+S GE +S+ I++  + + G K++  +     I TDN++   +V   +    +
Sbjct: 110 DYIYDQIVSIGEVVSTKIVAAWLNETGNKTLWADARNY-IQTDNSYREGKVDWAKTNQMI 168

Query: 175 KERLLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSG 234
           +  LLPLL + II V  GFIG T E Y TTLGR GSDYSAA+    L+A  + IW DV G
Sbjct: 169 QRDLLPLLNDNII-VTQGFIGGTSENYTTTLGREGSDYSAAIFASCLNAAALTIWKDVPG 227

Query: 235 VYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESE 294
           V   DP+      +I +LSY +A+EL Y+GA V+HP+TI+P   KGIP+ V++  +PE  
Sbjct: 228 VLNADPKWFDETEKIAQLSYHDAIELTYYGATVIHPKTIKPLQNKGIPLFVRSFIQPEGS 287

Query: 295 GTLIT---NDMEMSDSIVKAISTIKNVALINIFGAG-MVGVSGTAARIFKALGEEEVNVI 350
           GT IT   N + +   I K      N ALI+IF       +    + IF+     ++ + 
Sbjct: 288 GTAITKENNPLPIPSFIFKV-----NQALISIFPKDYSFIIEENLSNIFELFHTHKIKIN 342

Query: 351 LISQGSSETNISLVVSEEDVDKALKALKREFGDFGKKS-------FLNNNLIRDVSVDKD 403
            +   +   ++S+      ++K +K L  EF     K        + N   I  V+VDKD
Sbjct: 343 TMLNSAISFSVSVDDHPTQIEKLIKDLSEEFTVKYNKGLELVTIRYYNQQTIDRVTVDKD 402

Query: 404 V 404
           +
Sbjct: 403 I 403


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: 443
Number of extensions: 24
Number of successful extensions: 3
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: 422
Length adjustment: 33
Effective length of query: 440
Effective length of database: 389
Effective search space:   171160
Effective search space used:   171160
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 CA265_RS06275 CA265_RS06275 (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.9388.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    4.7e-88  282.1   0.0    5.7e-88  281.8   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS06275  CA265_RS06275 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS06275  CA265_RS06275 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.0   5.7e-88   5.7e-88       5     384 ..       3     386 ..       1     399 [. 0.94

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 5.7e-88
                                  TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekir 70 
                                                + KFGG Sv++++ +k+va+iv   k kg + ++V+SAm++vTd+L +l + + s+++  +++ ++i+
  lcl|FitnessBrowser__Pedo557:CA265_RS06275   3 IFKFGGASVKDADGVKNVANIVRDYK-KG-NLLIVISAMGKVTDKLEKLTQAFLSQNNeaHAIFDEIK 68 
                                                68******************998887.66.79********************99999878889999** PP

                                  TIGR00657  71 ekhlealeelasqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleel 128
                                                + h+++++el +   ++ + +++++ ++e+            +  +d i+s+GE +S++++aa+l+e 
  lcl|FitnessBrowser__Pedo557:CA265_RS06275  69 HFHFNIIDELFQ-GKANPVYDDVANTFVEIDWliedepdnneDYIYDQIVSIGEVVSTKIVAAWLNET 135
                                                ********9985.36778888888888888778889999999999*********************** PP

                                  TIGR00657 129 gvkavsllgaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRG 192
                                                g ++  + +a++ i td+++++ k    ++++++++ l++ll+ + i v++GFiG t+++++ttLGR 
  lcl|FitnessBrowser__Pedo557:CA265_RS06275 136 G-NKTLWADARNYIQTDNSYREGKvdwaKTNQMIQRDLLPLLNDN-IIVTQGFIGGTSENYTTTLGRE 201
                                                *.889999***************99999999************99.889******************* PP

                                  TIGR00657 193 GSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepa 260
                                                GSD++Aa+ A++l+A  + i++DV+G++ aDP+   e+ +++++sy+ a EL+++Ga v+hp+t++p+
  lcl|FitnessBrowser__Pedo557:CA265_RS06275 202 GSDYSAAIFASCLNAAALTIWKDVPGVLNADPKWFDETEKIAQLSYHDAIELTYYGATVIHPKTIKPL 269
                                                ******************************************************************** PP

                                  TIGR00657 261 mrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk...pgilaevfgal 325
                                                 +++ip++v+s  +pe+ GT i+++++   + ++ +  ++ nqal+s+  + +     + l+++f+  
  lcl|FitnessBrowser__Pedo557:CA265_RS06275 270 QNKGIPLFVRSFIQPEGSGTAITKENN---PLPIPSFIFKVNQALISIFPKDYSfiiEENLSNIFELF 334
                                                ************************955...689*****************9999999999******** PP

                                  TIGR00657 326 aeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvsl 384
                                                +++k++++++l    ++ isf v+ +d ++  e+l   +k++++  +v+++k+l lv++
  lcl|FitnessBrowser__Pedo557:CA265_RS06275 335 HTHKIKINTML----NSAISFSVSVDDHPTQIEKL---IKDLSEEFTVKYNKGLELVTI 386
                                                ***********....3369********99999996...7889999999*******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (422 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: 00:00:00.01
# Mc/sec: 12.59
//
[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