GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Leptospirillum ferrooxidans C2-3

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_014450628.1 LFE_RS12725 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_000284315.1:WP_014450628.1
          Length = 350

 Score =  315 bits (808), Expect = 8e-91
 Identities = 164/339 (48%), Positives = 236/339 (69%), Gaps = 13/339 (3%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEA-SPES 63
           L V + GATGAVG++M+  LE+R F +  L L +++RSAG KV+FKG+ +TV    +PE 
Sbjct: 7   LCVGIFGATGAVGKEMISILEERRFPVGELRLFATERSAGEKVSFKGRTITVSSFDNPEK 66

Query: 64  FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEH-- 121
            +G++IAL SAG + S  ++P    +G +VIDN+SAFRMD N PLVVPE+N + +  +  
Sbjct: 67  AKGIHIALLSAGATPSLEISPILRDQGILVIDNSSAFRMDPNVPLVVPEINPSKIPAYPA 126

Query: 122 NGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKE 181
             I+ANPNC+TIQM+ A++P+    G  +++V+T+Q+VSG G +A+ EL +Q   ILN  
Sbjct: 127 GAIVANPNCATIQMLLAIKPLIDCAGAKRIVVTTFQSVSGTGKDAMDELTTQLSLILNGR 186

Query: 182 --EIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAA 239
             ++ P++ P       +QIAFN +P ID F  +GYT EE KM+NET+KI+ M D++V A
Sbjct: 187 IGDVAPKVYP-------HQIAFNVLPHIDSFLPDGYTKEEEKMVNETRKILDMADIRVTA 239

Query: 240 TCVRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKN 299
           T VR+P+  GHSE+V IE +RD  + E  + +L++APGV + D+PS   YP+P D  G++
Sbjct: 240 TTVRVPVMVGHSEAVNIEFERD-LSPETARKILEKAPGVKVLDNPSDCEYPLPMDVAGQD 298

Query: 300 DVFVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAE 338
           DV+VGRIR+D    +G +LWVV DNL KGAA N+VQIAE
Sbjct: 299 DVYVGRIRRDFSVDHGLNLWVVGDNLRKGAALNAVQIAE 337


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: 317
Number of extensions: 15
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: 350
Length adjustment: 29
Effective length of query: 317
Effective length of database: 321
Effective search space:   101757
Effective search space used:   101757
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_014450628.1 LFE_RS12725 (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.3125345.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-134  434.4   0.0   1.7e-134  434.1   0.0    1.0  1  NCBI__GCF_000284315.1:WP_014450628.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014450628.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.1   0.0  1.7e-134  1.7e-134       2     334 ..       9     337 ..       8     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.1 bits;  conditional E-value: 1.7e-134
                             TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaek.esfegidialfsaGgsv 73 
                                           v+i GatGavG+e++ +Leer fp+ +l+l+a ersaG+kv fkg+ ++v++ ++ e+ +gi ial saG++ 
  NCBI__GCF_000284315.1:WP_014450628.1   9 VGIFGATGAVGKEMISILEERRFPVGELRLFATERSAGEKVSFKGRTITVSSFDNpEKAKGIHIALLSAGATP 81 
                                           89**************************************************86527999************* PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s e+ p    +g++viDn+safr+d++vPLvvpe+n +++   +   i+anPnC+tiq++ ++kpl d a+ k
  NCBI__GCF_000284315.1:WP_014450628.1  82 SLEISPILRDQGILVIDNSSAFRMDPNVPLVVPEINPSKIPAYPAGAIVANPNCATIQMLLAIKPLIDCAGAK 154
                                           ************************************************************************* PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           r+vv t+q+vsG+Gk++++eL+ q+  +l+g+  +     + +k +++qiafn++p+id++  dGytkee+k+
  NCBI__GCF_000284315.1:WP_014450628.1 155 RIVVTTFQSVSGTGKDAMDELTTQLSLILNGRIGD-----VAPKVYPHQIAFNVLPHIDSFLPDGYTKEEEKM 222
                                           *****************************999888.....599****************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           ++etrkil++ d++v+at+vrvPv++ghse+v+iefe++ls+e ++++L++apgv+v+d+ps+ +yp P++++
  NCBI__GCF_000284315.1:WP_014450628.1 223 VNETRKILDMADIRVTATTVRVPVMVGHSEAVNIEFERDLSPETARKILEKAPGVKVLDNPSDCEYPLPMDVA 295
                                           ************************************************************************* PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiae 334
                                           g+d+v+vgrir+D s ++gl+l+vv+DnlrkGaalnavqiae
  NCBI__GCF_000284315.1:WP_014450628.1 296 GQDDVYVGRIRRDFSVDHGLNLWVVGDNLRKGAALNAVQIAE 337
                                           *****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (350 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: 00:00:00.00
# Mc/sec: 19.85
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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