Alignments for a candidate for asd in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Archaeoglobus veneficus SNP6

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_013684774.1 ARCVE_RS10620 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q57658
         (354 letters)



>NCBI__GCF_000194625.1:WP_013684774.1
          Length = 342

 Score =  405 bits (1041), Expect = e-118
 Identities = 209/346 (60%), Positives = 264/346 (76%), Gaps = 9/346 (2%)

Query: 7   MKIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENI 66
           M+ KV VLGATG VGQ+F+QLL +HP FE++ALAASE+  GK Y +   W    ++PE +
Sbjct: 1   MRFKVAVLGATGMVGQKFIQLLENHPWFEISALAASEKRVGKPYGEEVNWLVSANVPECV 60

Query: 67  KDMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLV 126
           +DM ++P DPKH    D DIVFSALPS++A++ E  FAKEG ++ SNASA+RMEEDVPLV
Sbjct: 61  RDMEMVPMDPKHV---DADIVFSALPSNVAREVEAAFAKEGFVVASNASAFRMEEDVPLV 117

Query: 127 IPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAV 186
           IPEVN DHL+L+E Q++KRGWDG I+TNPNC+TI  VI+LKP+MD  GL+ V +A+MQA+
Sbjct: 118 IPEVNPDHLQLVETQKKKRGWDGFIVTNPNCTTIMLVISLKPLMD-LGLKTVRVASMQAL 176

Query: 187 SGAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAV 246
           SGAGY GVPSMAI DN+IPFIK EEEK++TE LKLLG     KV  A  K+SASC+RV V
Sbjct: 177 SGAGYPGVPSMAITDNVIPFIKGEEEKVETEPLKLLGKFDGKKVNPAPIKVSASCHRVPV 236

Query: 247 IDGHTESIFVKTKEGAEPEEIKEVMDKFDPLKDLNLPTY-AKPIVIREEIDRPQPRLDRN 305
           IDGHTE+++V   E      ++E +  F+ LK L+LPT   K I++R E DRPQPRLDR+
Sbjct: 237 IDGHTEAVWV---EFDRDVSVEEAIAAFESLKPLDLPTSPEKVIIVRSEPDRPQPRLDRD 293

Query: 306 EGNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVK 351
           EGNGMS+VVGR+RKD    +KY  + HNT+RGAAGAS+LNAE   K
Sbjct: 294 EGNGMSVVVGRVRKDS-NGLKYIVMGHNTVRGAAGASILNAELMAK 338


Lambda     K      H
   0.317    0.136    0.388 

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: 407
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: 354
Length of database: 342
Length adjustment: 29
Effective length of query: 325
Effective length of database: 313
Effective search space:   101725
Effective search space used:   101725
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_013684774.1 ARCVE_RS10620 (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.24701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-154  497.5   0.1     1e-153  497.3   0.1    1.0  1  lcl|NCBI__GCF_000194625.1:WP_013684774.1  ARCVE_RS10620 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013684774.1  ARCVE_RS10620 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.3   0.1    1e-153    1e-153       2     341 ..       4     337 ..       3     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 497.3 bits;  conditional E-value: 1e-153
                                 TIGR00978   2 kvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepaa 70 
                                               kvavLGatG+vGqk+++lle+hp+fe+ +++ase+++Gk yge v+w +s+++pe vrd+e++ ++p+ 
  lcl|NCBI__GCF_000194625.1:WP_013684774.1   4 KVAVLGATGMVGQKFIQLLENHPWFEISALAASEKRVGKPYGEEVNWLVSANVPECVRDMEMVPMDPK- 71 
                                               9******************************************************************9. PP

                                 TIGR00978  71 eekdvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.gwk 138
                                                + d+d+vfsalps+va+evE+++a+eG++v+snasa+R+++dvpl++pEvn+dhl+l+++qk++ gw+
  lcl|NCBI__GCF_000194625.1:WP_013684774.1  72 -HVDADIVFSALPSNVAREVEAAFAKEGFVVASNASAFRMEEDVPLVIPEVNPDHLQLVETQKKKrGWD 139
                                               .5589*********************************************************9999*** PP

                                 TIGR00978 139 GvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiekE 207
                                               G+ivtnpnC+t++l ++lkPl+   ++k v+va++qa+sGAGypGv+s++i+dnviP+ikgEEek+e+E
  lcl|NCBI__GCF_000194625.1:WP_013684774.1 140 GFIVTNPNCTTIMLVISLKPLM-DLGLKTVRVASMQALSGAGYPGVPSMAITDNVIPFIKGEEEKVETE 207
                                               **********************.89******************************************** PP

                                 TIGR00978 208 tkkilGkleegkvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglpsa 276
                                               ++k+lGk++++kv+pa+++vsa+++RvPv +GHte+v ve+d+++++ee+++a+++ k l    +lp+ 
  lcl|NCBI__GCF_000194625.1:WP_013684774.1 208 PLKLLGKFDGKKVNPAPIKVSASCHRVPVIDGHTEAVWVEFDRDVSVEEAIAAFESLKPL----DLPTS 272
                                               *******************************************************99988....9**** PP

                                 TIGR00978 277 PekpivlldeedrPqprldldaekgmavtvGrlreeseslklvvlghnlvRGAAGaallnaElly 341
                                               Pek+i+++ e+drPqprld+d ++gm+v+vGr+r++s+ lk++v+ghn+vRGAAGa++lnaEl+ 
  lcl|NCBI__GCF_000194625.1:WP_013684774.1 273 PEKVIIVRSEPDRPQPRLDRDEGNGMSVVVGRVRKDSNGLKYIVMGHNTVRGAAGASILNAELMA 337
                                               ***************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (342 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: 00:00:00.01
# Mc/sec: 9.46
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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