Alignments for a candidate for asd in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Clostridium acetobutylicum ATCC 824

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_010963889.1 CA_RS03110 aspartate-semialdehyde dehydrogenase

Query= BRENDA::Q4WWR8
         (363 letters)



>NCBI__GCF_000008765.1:WP_010963889.1
          Length = 359

 Score =  264 bits (674), Expect = 3e-75
 Identities = 149/364 (40%), Positives = 223/364 (61%), Gaps = 15/364 (4%)

Query: 6   KKKCGVLGATGSVGQRFILLLADHPFLELHAIGASNRSAGKKYKDAV--RWKQTTAMSER 63
           K + G+LG TG VGQRF  LL +HP+ E+  I AS RSAG+KY DAV  RWK    M E 
Sbjct: 4   KLRVGLLGGTGLVGQRFATLLDNHPYFEVTCIAASPRSAGQKYSDAVKGRWKLDIPMPEY 63

Query: 64  LSNLVLRDCR-ADQFS-DCDLVFSGLNSDVAG--EIEMEFIKAEIPVFSNAKNYRKHPLV 119
           + + +++D    D+ S + D VF  +N D +   +IE  + K EIPV SN   +R    V
Sbjct: 64  IKDFIVKDIYDIDEISKEVDFVFCAVNMDKSEIKKIEENYAKHEIPVVSNNSAHRFTEDV 123

Query: 120 PLVVPTVNPQHLDLIPHQRKEFGLKKGFLVCNSNCAVIGVVIPFAALQAKFGPVEEVEVF 179
           P+++P +NP+HLD+IP Q++  G KKGF+V   NC++   V   +AL  +F P  ++ V 
Sbjct: 124 PVIIPEINPEHLDIIPKQKERLGTKKGFIVAKPNCSIQSYVPAISAL-LEFKPT-KILVC 181

Query: 180 TEQAVSGAGYPGVPSMDIMDNVIPYISGEEDKLENEAQKILGSLNADATAFDEQKGLTVG 239
           T QA+SG+G       +I+DN IPYI GEE K E+E  K+ G +  +      +K   + 
Sbjct: 182 TYQAISGSGKTFEQFPEIVDNTIPYIPGEEQKSEDEPLKVWGHIEGNKIV--SKKDPLIT 239

Query: 240 ATCTRVGVTDGHMAFVSLRFKNRPGPSAEEVKQAMREYQSEAQKLGCPSAPREAIKVFDE 299
           + C RV V+DGH+A   + F+N+  P+ E++ + ++ Y+ + Q L  P+AP + I  F++
Sbjct: 240 SQCIRVAVSDGHLAATFVSFENK--PTKEQIVEKLKNYKGKPQLLNLPTAPEQFITYFED 297

Query: 300 PDRPQPRLDRDISKGYTVSVGRVREAAPGSYFDLRFAALSHNTVIGAAGSSILNAEVAVI 359
             RPQP+LDR+I KG  +S+GR+RE    + FD +F  LSHN + GAAG ++L AE+   
Sbjct: 298 EFRPQPKLDRNIEKGMGISIGRLRE---DTLFDYKFVGLSHNALRGAAGGAVLTAELLYK 354

Query: 360 KGYI 363
           +GY+
Sbjct: 355 EGYL 358


Lambda     K      H
   0.318    0.135    0.393 

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: 320
Number of extensions: 18
Number of successful extensions: 6
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: 363
Length of database: 359
Length adjustment: 29
Effective length of query: 334
Effective length of database: 330
Effective search space:   110220
Effective search space used:   110220
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_010963889.1 CA_RS03110 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR00978 (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/TIGR00978.hmm
# target sequence database:        /tmp/gapView.1252056.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00978  [M=342]
Accession:   TIGR00978
Description: asd_EA: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-108  348.3   0.0   2.6e-108  348.1   0.0    1.0  1  NCBI__GCF_000008765.1:WP_010963889.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008765.1:WP_010963889.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.1   0.0  2.6e-108  2.6e-108       1     342 []       5     354 ..       5     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 348.1 bits;  conditional E-value: 2.6e-108
                             TIGR00978   1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvk..wilsgdipeevrdleiketepaae 71 
                                           ++v++LG tGlvGq++  ll++hpyfe++ ++as+r+aG+ky+++vk  w+l+ ++pe+++d+ +k++ +  e
  NCBI__GCF_000008765.1:WP_010963889.1   5 LRVGLLGGTGLVGQRFATLLDNHPYFEVTCIAASPRSAGQKYSDAVKgrWKLDIPMPEYIKDFIVKDIYDIDE 77 
                                           69********************************************7558*****************998877 PP

                             TIGR00978  72 .ekdvdlvfsalpseva..eevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker..gwkG 139
                                            +k+vd vf a++ +++  +++E+++a++ ++v+sn sa+R+ +dvp+i+pE+n++hl+++ +qker    kG
  NCBI__GCF_000008765.1:WP_010963889.1  78 iSKEVDFVFCAVNMDKSeiKKIEENYAKHEIPVVSNNSAHRFTEDVPVIIPEINPEHLDIIPKQKERlgTKKG 150
                                           799********9877763369**********************************************96689* PP

                             TIGR00978 140 vivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiekEtkkil 212
                                           +iv+ pnCs+     a+  l+ ++  +k+ v t qa+sG G     + +i+dn+iPyi gEE+k e E++k+ 
  NCBI__GCF_000008765.1:WP_010963889.1 151 FIVAKPNCSIQSYVPAISALL-EFKPTKILVCTYQAISGSGKTFEQFPEIVDNTIPYIPGEEQKSEDEPLKVW 222
                                           *********************.9999*********************************************** PP

                             TIGR00978 213 Gkleegkve.paelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglpsaPekpivll 284
                                           G++e++k+  + +  ++ +++Rv v +GH+ + fv++++k   e+i+e+lk++k++pq l+lp+aPe+ i++ 
  NCBI__GCF_000008765.1:WP_010963889.1 223 GHIEGNKIVsKKDPLITSQCIRVAVSDGHLAATFVSFENKPTKEQIVEKLKNYKGKPQLLNLPTAPEQFITYF 295
                                           ******98615677899******************************************************** PP

                             TIGR00978 285 deedrPqprldldaekgmavtvGrlreese.slklvvlghnlvRGAAGaallnaEllyk 342
                                           ++e rPqp+ld+++ekgm +++Grlre++  + k+v l+hn +RGAAG a+l+aEllyk
  NCBI__GCF_000008765.1:WP_010963889.1 296 EDEFRPQPKLDRNIEKGMGISIGRLREDTLfDYKFVGLSHNALRGAAGGAVLTAELLYK 354
                                           *****************************99*************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (359 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.65
//
[ok]

This GapMind analysis is from Jul 25 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 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