Alignments for a candidate for asd in Halococcus hamelinensis 100A6

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Halococcus hamelinensis 100A6

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_007692528.1 C447_RS07535 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q57658
         (354 letters)



>NCBI__GCF_000336675.1:WP_007692528.1
          Length = 344

 Score =  312 bits (800), Expect = 7e-90
 Identities = 168/346 (48%), Positives = 230/346 (66%), Gaps = 5/346 (1%)

Query: 7   MKIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENI 66
           M  +VG+LGATG+VGQR VQLL  HP FE+  + AS+ SAG+ Y +A  W  D  +P+ +
Sbjct: 1   MTTRVGILGATGAVGQRLVQLLDPHPEFEIACVTASDDSAGRPYGEAANWRIDVPMPDAL 60

Query: 67  KDMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLV 126
            D+ V  T+P     +DV ++FS+LPS + ++ EP   + G ++ SN+S  RM +DVPL 
Sbjct: 61  ADLDVARTEPDAIP-DDVPLLFSSLPSAVGERVEPPLCEAGYVVSSNSSNDRMADDVPLT 119

Query: 127 IPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAV 186
           IPEVN DHL+LIE+QR+ R WDGA++ NPNCSTI AV  L  + + FGLE   +ATMQAV
Sbjct: 120 IPEVNGDHLDLIEVQRDSRDWDGALVKNPNCSTITAVPPLAALAE-FGLETAHVATMQAV 178

Query: 187 SGAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAV 246
           SG GY+GV SM I+DN++P I  EEEK++TE  KLLG     +V+     I+ASCNRVA 
Sbjct: 179 SGGGYSGVTSMEIIDNVLPHIGGEEEKVETEPTKLLGEFDGAEVKRHEVDIAASCNRVAT 238

Query: 247 IDGHTESIFVKTKEGAEPEEIKEVMDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNE 306
           +DGH ES++  T+E    ++    M +  P  DL+  +  + I + E+ DRPQPRLDR  
Sbjct: 239 VDGHLESVWADTREDITADDAARAMREL-PALDLH-SSPDQFIEVFEDPDRPQPRLDRMV 296

Query: 307 GNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKK 352
           G GMS+  G +R +    V++  L HNT+RGAAGASVLN E  V++
Sbjct: 297 GGGMSVAAGGLR-ETTRGVQFNCLAHNTLRGAAGASVLNGELLVER 341


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: 330
Number of extensions: 13
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: 344
Length adjustment: 29
Effective length of query: 325
Effective length of database: 315
Effective search space:   102375
Effective search space used:   102375
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_007692528.1 C447_RS07535 (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.642361.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-119  384.9   0.0   1.9e-119  384.7   0.0    1.0  1  NCBI__GCF_000336675.1:WP_007692528.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000336675.1:WP_007692528.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.7   0.0  1.9e-119  1.9e-119       2     341 ..       4     339 ..       3     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 384.7 bits;  conditional E-value: 1.9e-119
                             TIGR00978   2 kvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepaaeekd 74 
                                           +v++LGatG vGq+lv+ll+ hp+fe+a v+as+ +aG+ yge+++w ++ ++p+ + dl + +tep+a  +d
  NCBI__GCF_000336675.1:WP_007692528.1   4 RVGILGATGAVGQRLVQLLDPHPEFEIACVTASDDSAGRPYGEAANWRIDVPMPDALADLDVARTEPDAIPDD 76 
                                           8*******************************************************************9999* PP

                             TIGR00978  75 vdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.gwkGvivtnpn 146
                                           v l+fs+lps v e+vE+ l e+G++v sn+s+ R+ +dvpl +pEvn dhl+l++vq++  +w+G +v+npn
  NCBI__GCF_000336675.1:WP_007692528.1  77 VPLLFSSLPSAVGERVEPPLCEAGYVVSSNSSNDRMADDVPLTIPEVNGDHLDLIEVQRDSrDWDGALVKNPN 149
                                           **********************************************************9876*********** PP

                             TIGR00978 147 CstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiekEtkkilGkleegk 219
                                           Cst++   +l+ l  +++++  +vat+qavsG Gy+Gv+s++i+dnv+P+i+gEEek+e+E++k+lG++++ +
  NCBI__GCF_000336675.1:WP_007692528.1 150 CSTITAVPPLAALA-EFGLETAHVATMQAVSGGGYSGVTSMEIIDNVLPHIGGEEEKVETEPTKLLGEFDGAE 221
                                           *****999****99.9********************************************************* PP

                             TIGR00978 220 vepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglpsaPekpivlldeedrPqp 292
                                           v+  e++++a+++Rv +++GH+esv  ++ +++  +++ +a++e   l    +l+s P++ i + +++drPqp
  NCBI__GCF_000336675.1:WP_007692528.1 222 VKRHEVDIAASCNRVATVDGHLESVWADTREDITADDAARAMRELPAL----DLHSSPDQFIEVFEDPDRPQP 290
                                           ******************************************998776....9******************** PP

                             TIGR00978 293 rldldaekgmavtvGrlreeseslklvvlghnlvRGAAGaallnaElly 341
                                           rld+ +++gm+v  G lre+++ ++++ l+hn++RGAAGa++ln Ell+
  NCBI__GCF_000336675.1:WP_007692528.1 291 RLDRMVGGGMSVAAGGLRETTRGVQFNCLAHNTLRGAAGASVLNGELLV 339
                                           **********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (344 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: 21.93
//
[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