Alignments for a candidate for asd in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Azospirillum brasilense Sp245

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate AZOBR_RS13975 AZOBR_RS13975 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__azobra:AZOBR_RS13975
          Length = 339

 Score =  280 bits (716), Expect = 4e-80
 Identities = 149/336 (44%), Positives = 216/336 (64%), Gaps = 6/336 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTV-RVQNVEEFD 63
           + VA+ GATG VG  ML  L +R FP D +  LA++ + GK   F    V +V++V  FD
Sbjct: 3   YTVAVVGATGNVGREMLTTLADRRFPADAVIALAADSAVGKEVSFGEDAVLKVEDVGRFD 62

Query: 64  WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN 123
           +  V IALF+A  ++SA  AP  A AG VVID +  FR D D+PLV+PEVN +A+A +  
Sbjct: 63  FKGVDIALFAADAKVSAAHAPRGAAAGAVVIDASPQFRMDPDVPLVIPEVNGDALAGYAK 122

Query: 124 RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGY 183
           +NI+A+P  + I + +ALKP+++ V + R+ V+TYQ+ S AGK G+DEL GQT  +    
Sbjct: 123 KNIVASPGGAAILLAMALKPLHEQVTVSRVVVSTYQAASDAGKEGMDELFGQTRAIYVND 182

Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243
           P + + FS+QIAFN IP I  FM++G T++E  +  ET+K+  DP I V+ TCVRVPVF 
Sbjct: 183 PVQKSVFSKQIAFNVIPHIGPFMEDGATRDEWALTVETKKVL-DPKIKVSATCVRVPVFI 241

Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300
           GH+ A+ +E   P+ AE+   +L +  G+++        + T V +  G D V + R+R 
Sbjct: 242 GHSAAITIECVEPVTAEEARRILRKAPGMQVIDQQENDGYITPV-EIAGDDPVFISRIRE 300

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336
           D +  +G++ W   DN+RKGAA NAVQIAELLV++Y
Sbjct: 301 DYTVDNGLSFWASTDNLRKGAALNAVQIAELLVKEY 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: 306
Number of extensions: 17
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 AZOBR_RS13975 AZOBR_RS13975 (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.28566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-123  398.1   0.5   1.8e-123  397.9   0.5    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS13975  AZOBR_RS13975 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS13975  AZOBR_RS13975 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.9   0.5  1.8e-123  1.8e-123       2     339 .]       5     335 ..       4     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 397.9 bits;  conditional E-value: 1.8e-123
                                 TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgke.leveeaekesfegidialfsa 69 
                                               va+vGatG+vG+e+l++L++r fp+d++++la++ + Gk+v f +   l+ve++ +++f+g+dialf+a
  lcl|FitnessBrowser__azobra:AZOBR_RS13975   5 VAVVGATGNVGREMLTTLADRRFPADAVIALAADSAVGKEVSFGEDAvLKVEDVGRFDFKGVDIALFAA 73 
                                               9******************************************986538******************** PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                                + vs + ap+ a+ag++viD +  fr+d+dvPLv+pevn + l+   kk+i+a P  ++i l ++Lkp
  lcl|FitnessBrowser__azobra:AZOBR_RS13975  74 DAKVSAAHAPRGAAAGAVVIDASPQFRMDPDVPLVIPEVNGDALAGYAKKNIVASPGGAAILLAMALKP 142
                                               ********************************************************************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               l++++ + rvvvstYqa s aGk+g++eL  qt+a+++     p    ++ + f+kqiafn+ip+i+ +
  lcl|FitnessBrowser__azobra:AZOBR_RS13975 143 LHEQVTVSRVVVSTYQAASDAGKEGMDELFGQTRAIYVND---P----VQKSVFSKQIAFNVIPHIGPF 204
                                               ************************************9853...3....67899**************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                               +edG t++e  l+ et+k+l+ +++kvsatcvrvPvf+ghs +++ie  +++++ee++ +L++apg++v
  lcl|FitnessBrowser__azobra:AZOBR_RS13975 205 MEDGATRDEWALTVETKKVLD-PKIKVSATCVRVPVFIGHSAAITIECVEPVTAEEARRILRKAPGMQV 272
                                               *********************.*********************************************** PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339
                                               id+++++ y+tP+e++g d vf++rir+D + ++gl+ + ++DnlrkGaalnavqiaell+ke
  lcl|FitnessBrowser__azobra:AZOBR_RS13975 273 IDQQENDGYITPVEIAGDDPVFISRIREDYTVDNGLSFWASTDNLRKGAALNAVQIAELLVKE 335
                                               ************************************************************985 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.95
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code, or see 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