Alignments for a candidate for asd in Methanosarcina barkeri Fusaro

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Methanosarcina barkeri Fusaro

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011305787.1 MBAR_RS04125 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q57658
         (354 letters)



>NCBI__GCF_000195895.1:WP_011305787.1
          Length = 342

 Score =  405 bits (1041), Expect = e-118
 Identities = 206/340 (60%), Positives = 264/340 (77%), Gaps = 10/340 (2%)

Query: 9   IKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENIKD 68
           IK G+LGATG+VGQRFV+ LA+HP FE+TALAASERSAGK YK+A  W  D  +PE+++D
Sbjct: 4   IKAGILGATGAVGQRFVEALANHPWFEITALAASERSAGKTYKEAAGWRLDTAMPESVED 63

Query: 69  MVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVIP 128
           + V+P DPK     D D+VFSALP+DLA   EPEFAK G  + SNAS+YRME D+PLVIP
Sbjct: 64  IKVVPVDPKAV---DADVVFSALPADLALTVEPEFAKAGFAVASNASSYRMENDIPLVIP 120

Query: 129 EVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSG 188
           EVN +HL L+E+Q++ RGWDG IITNPNCSTI   +TLKP+M +FGLE   +ATMQA+SG
Sbjct: 121 EVNPEHLGLLEVQQDTRGWDGYIITNPNCSTIVMTVTLKPLM-QFGLETTQVATMQAISG 179

Query: 189 AGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAVID 248
           AG++GV +MAI DN+IP+I NEE+KM+TE+LKLLG     ++  A+ ++SASC+RV VID
Sbjct: 180 AGFSGVAAMAIYDNIIPYIGNEEKKMETETLKLLGEFNGSEIVPADMRVSASCHRVPVID 239

Query: 249 GHTESIFVKTKEGAEPEEIKEVMDKFDP-LKDLNLPTYAKPIVIREEIDRPQPRLDRNEG 307
           GHTE+I+   ++   PEE+++    FDP LK+L     AKP+++R+E DRPQPRLDRN G
Sbjct: 240 GHTEAIWAGMRDKPTPEEVRKAFLNFDPRLKELPSEP-AKPLIVRDESDRPQPRLDRNMG 298

Query: 308 NGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAE 347
            GMS+ VGRIR+     ++Y A+ HNTIRGAAGASVLNAE
Sbjct: 299 KGMSVSVGRIRE----GIRYIAMGHNTIRGAAGASVLNAE 334


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: 385
Number of extensions: 12
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_011305787.1 MBAR_RS04125 (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.29242.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-139  448.5   0.0   8.2e-139  448.4   0.0    1.0  1  lcl|NCBI__GCF_000195895.1:WP_011305787.1  MBAR_RS04125 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195895.1:WP_011305787.1  MBAR_RS04125 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.4   0.0  8.2e-139  8.2e-139       1     340 [.       4     336 ..       4     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.4 bits;  conditional E-value: 8.2e-139
                                 TIGR00978   1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepa 69 
                                               +k+++LGatG vGq++v+ l++hp+fe+++++aser+aGk+y+e++ w l++ +pe+v+d++++ ++p+
  lcl|NCBI__GCF_000195895.1:WP_011305787.1   4 IKAGILGATGAVGQRFVEALANHPWFEITALAASERSAGKTYKEAAGWRLDTAMPESVEDIKVVPVDPK 72 
                                               689****************************************************************** PP

                                 TIGR00978  70 aeekdvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.gw 137
                                               a+  d+d+vfsalp+++a  vE+++a++G+ v+snas++R+++d+pl++pEvn++hl ll+vq++  gw
  lcl|NCBI__GCF_000195895.1:WP_011305787.1  73 AV--DADVVFSALPADLALTVEPEFAKAGFAVASNASSYRMENDIPLVIPEVNPEHLGLLEVQQDTrGW 139
                                               87..78*******************************************************998766** PP

                                 TIGR00978 138 kGvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiek 206
                                               +G i+tnpnCst+++t++lkPl+ +++++  +vat+qa+sGAG++Gv++++i dn+iPyi+ EE+k+e+
  lcl|NCBI__GCF_000195895.1:WP_011305787.1 140 DGYIITNPNCSTIVMTVTLKPLM-QFGLETTQVATMQAISGAGFSGVAAMAIYDNIIPYIGNEEKKMET 207
                                               ***********************.9******************************************** PP

                                 TIGR00978 207 EtkkilGkleegkvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglps 275
                                               Et+k+lG++++ ++ pa++ vsa+++RvPv +GHte++   + +k  +ee+r+a+ +f+     ++lps
  lcl|NCBI__GCF_000195895.1:WP_011305787.1 208 ETLKLLGEFNGSEIVPADMRVSASCHRVPVIDGHTEAIWAGMRDKPTPEEVRKAFLNFDPR--LKELPS 274
                                               **********************************************************977..789*** PP

                                 TIGR00978 276 aPekpivlldeedrPqprldldaekgmavtvGrlreeseslklvvlghnlvRGAAGaallnaEll 340
                                                P kp++++de drPqprld++++kgm+v+vGr+re    ++++ +ghn++RGAAGa++lnaEll
  lcl|NCBI__GCF_000195895.1:WP_011305787.1 275 EPAKPLIVRDESDRPQPRLDRNMGKGMSVSVGRIRE---GIRYIAMGHNTIRGAAGASVLNAELL 336
                                               **********************************97...599*********************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.84
//
[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