Alignments for a candidate for asp-kinase in Pontibacter ramchanderi LP43

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pontibacter ramchanderi LP43

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_101443820.1 BD749_RS07650 aspartate kinase

Query= BRENDA::P08660
         (449 letters)



>NCBI__GCF_002846395.1:WP_101443820.1
          Length = 421

 Score =  173 bits (439), Expect = 8e-48
 Identities = 118/359 (32%), Positives = 180/359 (50%), Gaps = 12/359 (3%)

Query: 6   VSKFGGTSVADFDAMNRSADIVLSDANVR--LVVLSASAGITNLLVALAEGLEPGERF-E 62
           V KFGG SV D  A+   + IV +    +  L+V+SA    TN L  + +    G+ F E
Sbjct: 3   VFKFGGASVKDASALQNLSQIVSAQGGNKELLLVVSAMGKTTNALEQVYDLATAGQDFSE 62

Query: 63  KLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALT------DELVS 116
            L   R    AI+  L +PN      ERL      L +    + S  +T      D++VS
Sbjct: 63  ALQQSRQYHLAIVHEL-FPNREHPVYERLEHLFAQLQQVLQTSKSQLITNHDRGYDQVVS 121

Query: 117 HGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNE 176
            GEL+S+++    L+E+ +   W D RK ++T+  +  A  D A    +    L   L  
Sbjct: 122 FGELLSSVIVHYFLQEQGIANAWVDSRKYIQTDTTWREARVDWAWTERVIKRDLPALLEN 181

Query: 177 GLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSA 236
            L++TQGF+G  N G TTTLGR GSD++AA+ A  L A  + IW DV G+   DP+  + 
Sbjct: 182 QLIVTQGFLGGTNNGLTTTLGREGSDFSAAIFAYCLDAKGLYIWKDVAGLLNADPKRFAH 241

Query: 237 AKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENP 296
             R  E+ + E  EMA +GA V+HP T+ P     IP++V S  DP A GT +C+     
Sbjct: 242 TVRYRELDYQETVEMAYYGASVIHPKTIKPLANKSIPLYVKSFLDPTAEGTKICD-CRFE 300

Query: 297 PLFRALALRRNQTLLTLHSLNMLH-SRGFLAEVFGILARHNISVDLITTSEVSVALTLD 354
            L  A  ++ NQ L++  + +    S   L  +F  L+   + ++L+  S +S ++  D
Sbjct: 301 KLSPAYIVKDNQCLVSFSAKDFTFISEKNLGTIFNALSELRLKINLMQNSAISFSICTD 359


Lambda     K      H
   0.320    0.135    0.376 

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: 289
Number of extensions: 14
Number of successful extensions: 1
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: 449
Length of database: 421
Length adjustment: 32
Effective length of query: 417
Effective length of database: 389
Effective search space:   162213
Effective search space used:   162213
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: 51 (24.3 bits)

Align candidate WP_101443820.1 BD749_RS07650 (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.945943.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.1e-78  248.8   0.0    7.4e-78  248.5   0.0    1.1  1  NCBI__GCF_002846395.1:WP_101443820.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101443820.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.5   0.0   7.4e-78   7.4e-78       5     361 ..       3     369 ..       1     404 [. 0.86

  Alignments for each domain:
  == domain 1  score: 248.5 bits;  conditional E-value: 7.4e-78
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlea 76 
                                           V KFGG Sv+++  ++++ +iv+++   +++ + VvSAm+++T+aL ++ + +  +++  e +++ r+ hl++
  NCBI__GCF_002846395.1:WP_101443820.1   3 VFKFGGASVKDASALQNLSQIVSAQG-GNKELLLVVSAMGKTTNALEQVYDLATAGQDfSEALQQSRQYHLAI 74 
                                           89********************9998.677***************************988899********** PP

                             TIGR00657  77 leelasqalkeklkallekeleevkk.............ereldlilsvGEklSaallaaaleelgvkavsll 136
                                           ++el ++   + + + le+ ++++++             +r +d ++s+GE lS+ ++   l+e+g  a +++
  NCBI__GCF_002846395.1:WP_101443820.1  75 VHELFPNRE-HPVYERLEHLFAQLQQvlqtsksqlitnhDRGYDQVVSFGELLSSVIVHYFLQEQG-IANAWV 145
                                           ***995433.33333344444444444556999*********************************.88899* PP

                             TIGR00657 137 gaeagiltdsefgrAk...vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalk 206
                                           ++++ i td ++++A+   + +e   +r +++l e+++ v++GF+G t++g +ttLGR GSD++Aa+ A +l+
  NCBI__GCF_002846395.1:WP_101443820.1 146 DSRKYIQTDTTWREARvdwAWTERVIKRDLPALLENQLIVTQGFLGGTNNGLTTTLGREGSDFSAAIFAYCLD 218
                                           ****************998777777777788888888************************************ PP

                             TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeG 279
                                           A+ + i++DV G + aDP+    + r  e++y+E +E+a++Ga v+hp+t++p+++++ip+ vks  +p+aeG
  NCBI__GCF_002846395.1:WP_101443820.1 219 AKGLYIWKDVAGLLNADPKRFAHTVRYRELDYQETVEMAYYGASVIHPKTIKPLANKSIPLYVKSFLDPTAEG 291
                                           ************************************************************************* PP

                             TIGR00657 280 Tlivakskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvd 349
                                           T i+  +    e+   a  +++nq lvs s +       + l ++f+al+e + +++l+  +s    isf + 
  NCBI__GCF_002846395.1:WP_101443820.1 292 TKICDCRF---EKLSPAYIVKDNQCLVSFSAKDFTfisEKNLGTIFNALSELRLKINLMQ-NS---AISFSIC 357
                                           *****955...4677888999999999999999988889999****************98.32...3666666 PP

                             TIGR00657 350 kedadkakellk 361
                                           ++  ++  ++l 
  NCBI__GCF_002846395.1:WP_101443820.1 358 TDYNEERLQKLL 369
                                           555444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (421 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: 14.83
//
[ok]

This GapMind analysis is from Jul 26 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