GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Escherichia coli BW25113

Align aspartate-semialdehyde dehydrogenase (characterized)
to candidate 17495 b3433 aspartate-semialdehyde dehydrogenase (NCBI)

Query= CharProtDB::CH_024631
         (367 letters)



>FitnessBrowser__Keio:17495
          Length = 367

 Score =  736 bits (1900), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDL 60
           MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDL
Sbjct: 1   MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDL 60

Query: 61  EALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVIT 120
           EALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVIT
Sbjct: 61  EALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVIT 120

Query: 121 DGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMG 180
           DGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMG
Sbjct: 121 DGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMG 180

Query: 181 HLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSR 240
           HLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSR
Sbjct: 181 HLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSR 240

Query: 241 EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNP 300
           EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNP
Sbjct: 241 EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNP 300

Query: 301 WAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLR 360
           WAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLR
Sbjct: 301 WAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLR 360

Query: 361 RMLRQLA 367
           RMLRQLA
Sbjct: 361 RMLRQLA 367


Lambda     K      H
   0.319    0.136    0.409 

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: 625
Number of extensions: 13
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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: 49 (23.5 bits)

Align candidate 17495 b3433 (aspartate-semialdehyde dehydrogenase (NCBI))
to HMM TIGR01745 (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/TIGR01745.hmm
# target sequence database:        /tmp/gapView.27233.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01745  [M=366]
Accession:   TIGR01745
Description: asd_gamma: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.5e-231  751.6   0.0   7.3e-231  751.4   0.0    1.0  1  lcl|FitnessBrowser__Keio:17495  b3433 aspartate-semialdehyde deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17495  b3433 aspartate-semialdehyde dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  751.4   0.0  7.3e-231  7.3e-231       1     365 [.       2     366 ..       2     367 .] 1.00

  Alignments for each domain:
  == domain 1  score: 751.4 bits;  conditional E-value: 7.3e-231
                       TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqggdytke 79 
                                     k+vg++gwrgmvgsvl++rm+ee+dfdai+pvffstsqlgq+aps+++++++l+da+d++alk+ldii+tcqggdyt+e
  lcl|FitnessBrowser__Keio:17495   2 KNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNE 80 
                                     69***************************************************************************** PP

                       TIGR01745  80 iypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrdelvewvsva 158
                                     iypklr++gw+gywidaasslrmkdda+iildpvn+dvi+d++n+girtfvggnctvsl+lmslgglf+++lv+wvsva
  lcl|FitnessBrowser__Keio:17495  81 IYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVA 159
                                     ******************************************************************************* PP

                       TIGR01745 159 tyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplagslipwidkqldngq 237
                                     tyqaasgggarhmrell+qmg+ly++v++ela+pssail+ierkvt+l+rs+elpv+nf+vplagslipwidkqldngq
  lcl|FitnessBrowser__Keio:17495 160 TYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQ 238
                                     ******************************************************************************* PP

                       TIGR01745 238 sreewkgqaetnkilgtkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlrelt 316
                                     sreewkgqaetnkil+t+++i+vdglcvr+galrchsqa+tiklkkdvs++++ee+++ahn+w+kvvpn+reit+relt
  lcl|FitnessBrowser__Keio:17495 239 SREEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELT 317
                                     ******************************************************************************* PP

                       TIGR01745 317 paavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365
                                     paavtgtl++pvgrlrklnmg+e+lsaftvgdqllwgaaeplrrmlr+l
  lcl|FitnessBrowser__Keio:17495 318 PAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL 366
                                     ***********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (367 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: 12.35
//
[ok]

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

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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