GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Salinicoccus carnicancri Crm

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_017549001.1 C792_RS0108270 aspartate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-6564
         (346 letters)



>NCBI__GCF_000330705.1:WP_017549001.1
          Length = 326

 Score =  277 bits (709), Expect = 2e-79
 Identities = 150/337 (44%), Positives = 217/337 (64%), Gaps = 17/337 (5%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPES- 63
           + VA+VGATG VG +M++  E    + D +TLLSS RSAG  +   G+ELTVQE + E+ 
Sbjct: 2   VRVAIVGATGVVGTKMIEMFEQYGIKADEITLLSSARSAGKSLQVMGEELTVQELTEETP 61

Query: 64  FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNG 123
            +G +  + SAGGS S+  AP   + G+IVIDN+S +RM E+  L+VPE+N   L     
Sbjct: 62  KQGFDYVVMSAGGSTSRQFAPLFEENGSIVIDNSSQWRMHEDIDLIVPEINAPKLDRK-- 119

Query: 124 IIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEI 183
           IIANPNCSTIQ V AL+P+++ +GL +V  +TYQAVSG+G+  +++L          EE 
Sbjct: 120 IIANPNCSTIQSVVALQPLKEKFGLKRVNYTTYQAVSGSGSGGLRDL----------EEG 169

Query: 184 EPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243
                P    +  Y    N +P ID F +NGYT EE KMI+ET+KI+ +PDL V+ATCVR
Sbjct: 170 ARGEAPTTYPRPIYD---NVLPHIDVFLENGYTKEEQKMIDETRKILGLPDLAVSATCVR 226

Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303
           +P+   HS  + + ++ ++AT E++++  +  P + L D+P    YP P ++ G+ +VFV
Sbjct: 227 VPVSNSHSVHMNVTLE-NEATEEEVRDAFRNIPHIMLLDNPESNEYPTPLESTGRPEVFV 285

Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340
           GRIR+D    N FH+W  +DN+LKGAA NSVQI + +
Sbjct: 286 GRIRRDDSLGNTFHVWCTADNILKGAAQNSVQILKQI 322


Lambda     K      H
   0.314    0.131    0.366 

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: 297
Number of extensions: 14
Number of successful extensions: 5
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: 346
Length of database: 326
Length adjustment: 28
Effective length of query: 318
Effective length of database: 298
Effective search space:    94764
Effective search space used:    94764
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_017549001.1 C792_RS0108270 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.59271.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: aspartate-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-115  369.8   0.0   1.5e-114  368.6   0.0    1.5  1  NCBI__GCF_000330705.1:WP_017549001.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017549001.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.6   0.0  1.5e-114  1.5e-114       1     336 [.       3     322 ..       3     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 368.6 bits;  conditional E-value: 1.5e-114
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg.idialfsaGgs 72 
                                           +vaivGatG vG ++++++e+   ++d+++ll+s+rsaGk +++ g+el+v+e+++e++++  d  ++saGgs
  NCBI__GCF_000330705.1:WP_017549001.1   3 RVAIVGATGVVGTKMIEMFEQYGIKADEITLLSSARSAGKSLQVMGEELTVQELTEETPKQgFDYVVMSAGGS 75 
                                           69*******************************************************88766*********** PP

                             TIGR01296  73 vskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeakl 145
                                           +s++fap + ++g iviDn+s +r+ ed+ L+vpe+na +l  +    iianPnCstiq vv+L+plk++++l
  NCBI__GCF_000330705.1:WP_017549001.1  76 TSRQFAPLFEENGSIVIDNSSQWRMHEDIDLIVPEINAPKLD-R---KIIANPNCSTIQSVVALQPLKEKFGL 144
                                           *************************************99874.4...59************************ PP

                             TIGR01296 146 krvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelk 218
                                           krv   tYqavsG+G  g+ +L++ ++      e         + +++++i  n++p+id + e+Gytkee+k
  NCBI__GCF_000330705.1:WP_017549001.1 145 KRVNYTTYQAVSGSGSGGLRDLEEGARG-----EA--------PTTYPRPIYDNVLPHIDVFLENGYTKEEQK 204
                                           ***********************99875.....33........479*************************** PP

                             TIGR01296 219 llfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPlea 291
                                           ++ etrkilg +dl vsatcvrvPv  +hs+ +++ +e+e++ eev++ +++ p ++++d+p++n+yptPle 
  NCBI__GCF_000330705.1:WP_017549001.1 205 MIDETRKILGLPDLAVSATCVRVPVSNSHSVHMNVTLENEATEEEVRDAFRNIPHIMLLDNPESNEYPTPLES 277
                                           ************************************************************************* PP

                             TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336
                                           +g+ evfvgrir+D s +++++++++aDn++kGaa n+vqi +++
  NCBI__GCF_000330705.1:WP_017549001.1 278 TGRPEVFVGRIRRDDSLGNTFHVWCTADNILKGAAQNSVQILKQI 322
                                           *****************************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (326 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 5.60
//
[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:

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:

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:

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:

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