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_010963351.1 CA_RS00135 aspartate-semialdehyde dehydrogenase

Query= BRENDA::Q4WWR8
         (363 letters)



>NCBI__GCF_000008765.1:WP_010963351.1
          Length = 360

 Score =  251 bits (641), Expect = 2e-71
 Identities = 148/364 (40%), Positives = 211/364 (57%), Gaps = 15/364 (4%)

Query: 6   KKKCGVLGATGSVGQRFILLLADHPFLELHAIGASNRSAGKKYKDAV--RWKQTTAMSER 63
           K + G++G TG VGQRF  LL DHP+ E+  I AS +SAG  Y++AV  RWK    + E 
Sbjct: 3   KLRVGLIGGTGMVGQRFACLLKDHPWFEVTLIAASKKSAGLTYEEAVKDRWKMNEPIPEG 62

Query: 64  LSNLVLRDC-RADQFSDC-DLVFSG--LNSDVAGEIEMEFIKAEIPVFSNAKNYRKHPLV 119
           + NL+++D    D+ S   D VF    LN +    +E ++ K E+PV SN    R    V
Sbjct: 63  VKNLIVKDAFDVDEISSMVDFVFCAISLNKEETRLLEEDYAKHEMPVISNNSANRYVQDV 122

Query: 120 PLVVPTVNPQHLDLIPHQRKEFGLKKGFLVCNSNCAVIGVVIPFAALQAKFGPVEEVEVF 179
           P+++P +N  H ++I  Q+K  G K+GF+    NC++   V P +AL  K+ P E +   
Sbjct: 123 PVLIPEINNNHTEIIDIQKKRLGTKRGFISVKPNCSIQSYVPPISAL-LKYEP-ETILAC 180

Query: 180 TEQAVSGAGYPGVPSMDIMDNVIPYISGEEDKLENEAQKILGSLNADATAFDEQKGLTVG 239
           T QA+SGAG       +I+DNVIPYI GEE+K ENE  KI G +  +         +T  
Sbjct: 181 TYQAISGAGKTFKECPEILDNVIPYIKGEEEKSENEPLKIWGKIENNKIVNASSPLITT- 239

Query: 240 ATCTRVGVTDGHMAFVSLRFKNRPGPSAEEVKQAMREYQSEAQKLGCPSAPREAIKVFDE 299
             C RV VTDGH+A V + FK +P  S +E+  A   +++    L  PSAP++ +  FDE
Sbjct: 240 -QCIRVPVTDGHLAAVFVNFKTKP--SKQEIIDAWENFKAPECALNLPSAPKKFLHYFDE 296

Query: 300 PDRPQPRLDRDISKGYTVSVGRVREAAPGSYFDLRFAALSHNTVIGAAGSSILNAEVAVI 359
           PDRPQ +LDRD   G  +++GR+RE      F  +F  LSHNT+ GAAG  +L+AE+   
Sbjct: 297 PDRPQTKLDRDFENGMGITMGRLRE---DKLFQYKFVCLSHNTLRGAAGGGVLSAELLKT 353

Query: 360 KGYI 363
           +GY+
Sbjct: 354 QGYL 357


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: 254
Number of extensions: 14
Number of successful extensions: 7
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: 360
Length adjustment: 29
Effective length of query: 334
Effective length of database: 331
Effective search space:   110554
Effective search space used:   110554
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_010963351.1 CA_RS00135 (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.278163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-102  329.4   0.0   1.4e-102  329.2   0.0    1.0  1  NCBI__GCF_000008765.1:WP_010963351.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008765.1:WP_010963351.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.2   0.0  1.4e-102  1.4e-102       1     341 [.       4     352 ..       4     353 .. 0.96

  Alignments for each domain:
  == domain 1  score: 329.2 bits;  conditional E-value: 1.4e-102
                             TIGR00978   1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvk..wilsgdipeevrdleiketepaae 71 
                                           ++v+++G tG+vGq++  ll+ hp+fe++ ++as+++aG +y+e+vk  w+++ +ipe v++l +k+  ++ e
  NCBI__GCF_000008765.1:WP_010963351.1   4 LRVGLIGGTGMVGQRFACLLKDHPWFEVTLIAASKKSAGLTYEEAVKdrWKMNEPIPEGVKNLIVKDAFDVDE 76 
                                           69********************************************75579***************9988866 PP

                             TIGR00978  72 .ekdvdlvfsa..lpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker..gwkG 139
                                            +  vd vf a  l++e ++ +E+ +a++ ++v+sn sa+R+ +dvp+++pE+n++h e+++ qk+r    +G
  NCBI__GCF_000008765.1:WP_010963351.1  77 iSSMVDFVFCAisLNKEETRLLEEDYAKHEMPVISNNSANRYVQDVPVLIPEINNNHTEIIDIQKKRlgTKRG 149
                                           6889*****993345777899**********************************************96679* PP

                             TIGR00978 140 vivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiekEtkkil 212
                                           +i   pnCs+     ++  l+ ++  + +   t qa+sGAG       +ildnviPyikgEEek e+E++ki 
  NCBI__GCF_000008765.1:WP_010963351.1 150 FISVKPNCSIQSYVPPISALL-KYEPETILACTYQAISGAGKTFKECPEILDNVIPYIKGEEEKSENEPLKIW 221
                                           *********************.99************************************************* PP

                             TIGR00978 213 Gkleegkvepaele.vsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglpsaPekpivll 284
                                           Gk+e++k+ +a+   ++ +++RvPv++GH+ +vfv+++ k + +ei++a+++fk     l+lpsaP+k + + 
  NCBI__GCF_000008765.1:WP_010963351.1 222 GKIENNKIVNASSPlITTQCIRVPVTDGHLAAVFVNFKTKPSKQEIIDAWENFKAPECALNLPSAPKKFLHYF 294
                                           ********99987627889****************************************************** PP

                             TIGR00978 285 deedrPqprldldaekgmavtvGrlreese.slklvvlghnlvRGAAGaallnaElly 341
                                           de+drPq++ld+d e+gm +t+Grlre++  + k+v l+hn++RGAAG  +l+aEll+
  NCBI__GCF_000008765.1:WP_010963351.1 295 DEPDRPQTKLDRDFENGMGITMGRLREDKLfQYKFVCLSHNTLRGAAGGGVLSAELLK 352
                                           *****************************99************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (360 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.39
//
[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