Alignments for a candidate for asd in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Pyrolobus fumarii 1A

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_014026421.1 PYRFU_RS04350 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q57658
         (354 letters)



>NCBI__GCF_000223395.1:WP_014026421.1
          Length = 352

 Score =  331 bits (848), Expect = 2e-95
 Identities = 171/346 (49%), Positives = 228/346 (65%), Gaps = 1/346 (0%)

Query: 8   KIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENIK 67
           K++  VLGATG VGQ FV+LL +HPMFE+  +AASERSAG+ Y +A  W      PE++ 
Sbjct: 4   KLRAAVLGATGLVGQMFVKLLDEHPMFEIVYVAASERSAGRSYCEAVNWVLGGSPPESLC 63

Query: 68  DMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVI 127
            + V      +    +VD+VFSALPS +A + E   A+ G  + SNAS  R+EEDVPL++
Sbjct: 64  GIKVEKVGVDNVPKSEVDVVFSALPSSVAGEIEAGLARRGFTVVSNASPMRLEEDVPLLV 123

Query: 128 PEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVS 187
           PE+N DH+ L++IQR++RGW GAI  NPNCS+   V++LKP++D FGLE V + TMQAVS
Sbjct: 124 PEINWDHVGLVKIQRQRRGWSGAIYKNPNCSSAILVLSLKPLLDNFGLEKVLVTTMQAVS 183

Query: 188 GAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAVI 247
           GAGYNGVPSMAILDN++PFI  EEEK+  E  K+LG  +  +VE A F I A+  RV V+
Sbjct: 184 GAGYNGVPSMAILDNIVPFIAKEEEKLANEPRKILGVYRGDRVEWARFTIHATTTRVPVL 243

Query: 248 DGHTESIFVKTKEGAEPEEIKEVMDKFDPL-KDLNLPTYAKPIVIREEIDRPQPRLDRNE 306
            GH ES++    + A  E++ +  + + P   +       KP+V R E+DRPQPRLDR E
Sbjct: 244 HGHLESVYAYLSKPASVEDVVQAWESWRPWGSEKPFMAPEKPVVYRREVDRPQPRLDRME 303

Query: 307 GNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKK 352
           G GMS V GR R      + Y  L HN IRGAAG ++L AE   ++
Sbjct: 304 GGGMSSVTGRARMVEDRLLAYLVLGHNLIRGAAGNAILIAEMLARE 349


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: 333
Number of extensions: 11
Number of successful extensions: 2
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: 352
Length adjustment: 29
Effective length of query: 325
Effective length of database: 323
Effective search space:   104975
Effective search space used:   104975
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_014026421.1 PYRFU_RS04350 (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.13453.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-135  437.2   0.0   2.3e-135  437.0   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_014026421.1  PYRFU_RS04350 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014026421.1  PYRFU_RS04350 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.0   0.0  2.3e-135  2.3e-135       1     340 [.       5     346 ..       5     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 437.0 bits;  conditional E-value: 2.3e-135
                                 TIGR00978   1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepa 69 
                                               +++avLGatGlvGq +vkll++hp+fe++ v+aser+aG++y e+v+w+l g  pe++ +++++++  +
  lcl|NCBI__GCF_000223395.1:WP_014026421.1   5 LRAAVLGATGLVGQMFVKLLDEHPMFEIVYVAASERSAGRSYCEAVNWVLGGSPPESLCGIKVEKVGVD 73 
                                               689**************************************************************9988 PP

                                 TIGR00978  70 ae.ekdvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.g 136
                                                + + +vd+vfsalps+va+e+E+ la++G++v+snas++Rl++dvpl+vpE+n+dh+ l+k q++r g
  lcl|NCBI__GCF_000223395.1:WP_014026421.1  74 NVpKSEVDVVFSALPSSVAGEIEAGLARRGFTVVSNASPMRLEEDVPLLVPEINWDHVGLVKIQRQRrG 142
                                               777999***********************************************************999* PP

                                 TIGR00978 137 wkGvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekie 205
                                               w+G i +npnCs ail l+lkPl+d+++++kv v+t+qavsGAGy+Gv+s++ildn++P+i +EEek++
  lcl|NCBI__GCF_000223395.1:WP_014026421.1 143 WSGAIYKNPNCSSAILVLSLKPLLDNFGLEKVLVTTMQAVSGAGYNGVPSMAILDNIVPFIAKEEEKLA 211
                                               ********************************************************************* PP

                                 TIGR00978 206 kEtkkilGkleegkvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglp 274
                                               +E++kilG  ++++ve a + + atttRvPvl+GH+esv+  l+k  ++e++++a+++++    ++ + 
  lcl|NCBI__GCF_000223395.1:WP_014026421.1 212 NEPRKILGVYRGDRVEWARFTIHATTTRVPVLHGHLESVYAYLSKPASVEDVVQAWESWRPWGSEKPF- 279
                                               *************************************************************9777766. PP

                                 TIGR00978 275 saPekpivlldeedrPqprldldaekgmavtvGrlreese.slklvvlghnlvRGAAGaallnaEll 340
                                                aPekp+v+++e drPqprld+  ++gm+ + Gr r  ++  l + vlghnl+RGAAG a+l aE+l
  lcl|NCBI__GCF_000223395.1:WP_014026421.1 280 MAPEKPVVYRREVDRPQPRLDRMEGGGMSSVTGRARMVEDrLLAYLVLGHNLIRGAAGNAILIAEML 346
                                               689*********************************9988799**********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (352 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: 8.50
//
[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