Alignments for a candidate for asd in Azospirillum sp. B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Azospirillum sp. B510

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_012974960.1 AZL_RS12765 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_000010725.1:WP_012974960.1
          Length = 339

 Score =  326 bits (836), Expect = 5e-94
 Identities = 178/336 (52%), Positives = 227/336 (67%), Gaps = 6/336 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTV-RVQNVEEFD 63
           + VA+ GATG VG  +L+ L ER+FP D +  LASE+S G+   +    + +VQ++ +FD
Sbjct: 3   YTVAVIGATGNVGREILQTLAERKFPADTVIALASEKSIGQEVSYGEDDILKVQDLNKFD 62

Query: 64  WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN 123
           +  V I L S G ++SA   P AA AG VVIDNTS FR D D+PLVVPEVNPEA+A +R 
Sbjct: 63  FHGVDIVLSSPGAKVSAVHVPRAAAAGAVVIDNTSQFRMDPDVPLVVPEVNPEALAGYRK 122

Query: 124 RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGY 183
           R IIANPNCSTIQM VALKP++D   I R+ V+TYQSVSGAGK  +DEL  QT  +    
Sbjct: 123 RGIIANPNCSTIQMAVALKPLHDRFKIHRVVVSTYQSVSGAGKEAMDELFTQTRAIFVND 182

Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243
           P   + F +QIAFN IP ID FM++G TKEE KM  ET+KI  DP I V  TCVRVP F 
Sbjct: 183 PVAKSVFPKQIAFNVIPHIDVFMEDGSTKEEWKMTVETKKIL-DPKIKVAATCVRVPTFI 241

Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300
           GHA ++++ET  PI AE+   +L    G+ +     G  + T V +  G + V V R+R+
Sbjct: 242 GHALSINIETEEPISAEEARVVLRAAPGLSVVDQQTGEGYVTPV-EVAGDNPVFVSRIRD 300

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336
           DI+  +G++ W VADN+RKGAA NAVQIAELLVRDY
Sbjct: 301 DITVENGLSFWCVADNLRKGAALNAVQIAELLVRDY 336


Lambda     K      H
   0.319    0.135    0.395 

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: 329
Number of extensions: 12
Number of successful extensions: 4
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: 337
Length of database: 339
Length adjustment: 28
Effective length of query: 309
Effective length of database: 311
Effective search space:    96099
Effective search space used:    96099
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_012974960.1 AZL_RS12765 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.3621292.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.4e-142  458.4   1.6   8.4e-142  458.2   1.6    1.0  1  NCBI__GCF_000010725.1:WP_012974960.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010725.1:WP_012974960.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.2   1.6  8.4e-142  8.4e-142       2     338 ..       5     334 ..       4     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 458.2 bits;  conditional E-value: 8.4e-142
                             TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgke.leveeaekesfegidialfsaGgsv 73 
                                           va++GatG+vG+e+l++L+er+fp+d++++lase+s G++v + + + l+v++++k++f+g+di l s G+ v
  NCBI__GCF_000010725.1:WP_012974960.1   5 VAVIGATGNVGREILQTLAERKFPADTVIALASEKSIGQEVSYGEDDiLKVQDLNKFDFHGVDIVLSSPGAKV 77 
                                           9*****************************************98765279*********************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s + +p+aa+ag++viDnts fr+d+dvPLvvpevn e l+  +k+giianPnCstiq+ v+Lkpl+d++k++
  NCBI__GCF_000010725.1:WP_012974960.1  78 SAVHVPRAAAAGAVVIDNTSQFRMDPDVPLVVPEVNPEALAGYRKRGIIANPNCSTIQMAVALKPLHDRFKIH 150
                                           ************************************************************************* PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           rvvvstYq+vsGaGk++++eL  qt+a+++     p    +  + f+kqiafn+ip+id ++edG tkee k+
  NCBI__GCF_000010725.1:WP_012974960.1 151 RVVVSTYQSVSGAGKEAMDELFTQTRAIFVND---P----VAKSVFPKQIAFNVIPHIDVFMEDGSTKEEWKM 216
                                           ***************************99754...3....56789**************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           + et+kil+ +++kv+atcvrvP f+gh++s++ie+e+++s+ee++ +L+ apg+ v+d++ ++ y+tP+e++
  NCBI__GCF_000010725.1:WP_012974960.1 217 TVETKKILD-PKIKVAATCVRVPTFIGHALSINIETEEPISAEEARVVLRAAPGLSVVDQQTGEGYVTPVEVA 288
                                           *********.*************************************************************** PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                           g + vfv+rir D++ e+gl+ ++vaDnlrkGaalnavqiaell++
  NCBI__GCF_000010725.1:WP_012974960.1 289 GDNPVFVSRIRDDITVENGLSFWCVADNLRKGAALNAVQIAELLVR 334
                                           *******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (339 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.75
//
[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