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 (EC 1.2.1.11) (characterized)
to candidate AZOBR_RS14735 AZOBR_RS14735 aspartate-semialdehyde dehydrogenase

Query= metacyc::AT1G14810-MONOMER
         (375 letters)



>FitnessBrowser__azobra:AZOBR_RS14735
          Length = 337

 Score =  290 bits (741), Expect = 5e-83
 Identities = 157/345 (45%), Positives = 215/345 (62%), Gaps = 11/345 (3%)

Query: 34  LQESAPS---LAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTV 90
           +  S+PS   +A+VG TGAVG+E + VL  R FP + + + AS+RSAG+ V     E T+
Sbjct: 1   MSTSSPSPRRVAIVGATGAVGREMVDVLHRRSFPVAELGLFASERSAGRTVETPFGEKTL 60

Query: 91  EELTADSFNGVDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPE 150
                +   G DI L +  G  +KE  P  A  G +V+DNSSAFR  D VPL++PE+N  
Sbjct: 61  VAFDVEKVKGYDIVLLAVSGDFAKEHAPAIAAGGALVIDNSSAFRYDDNVPLIVPEINAH 120

Query: 151 AMKGIKVGMGKGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEEL 210
           AM       G   LIANPNC+T I ++A+ PLH    +KR++VSTYQA SGAGA  M EL
Sbjct: 121 AM-------GDAKLIANPNCTTAIAVVALGPLHKAFGLKRVIVSTYQATSGAGAEGMAEL 173

Query: 211 VQQTREVLEGKPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKV 270
            +QTR  L+GKP   ++F     FNL        +NGY +EEMK+  ETRKI    ++ V
Sbjct: 174 EEQTRNQLDGKPVVNSVFRHPIPFNLIPQIDAFQENGYTKEEMKVTWETRKILEIPDLPV 233

Query: 271 TATCIRVPVMRAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNK 330
           + T +R+P  RAH+E++ ++  +P+  + AR +L  APGV + D  A   +P PL+ + +
Sbjct: 234 SCTAVRIPTYRAHSEAITVETLSPVTPDAARAVLADAPGVVVKDVPADGVYPMPLNATGQ 293

Query: 331 DDVAVGRIRRDVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375
            DV VGRIR  +   G+ GLD+FVCGDQ+ KGAALNAVQIAE+ L
Sbjct: 294 FDVEVGRIRTSLI-FGDHGLDLFVCGDQLLKGAALNAVQIAELSL 337


Lambda     K      H
   0.318    0.133    0.380 

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: 336
Number of extensions: 14
Number of successful extensions: 3
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: 375
Length of database: 337
Length adjustment: 29
Effective length of query: 346
Effective length of database: 308
Effective search space:   106568
Effective search space used:   106568
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate AZOBR_RS14735 AZOBR_RS14735 (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.23735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-118  379.2   0.0     1e-117  379.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS14735  AZOBR_RS14735 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS14735  AZOBR_RS14735 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.0   0.0    1e-117    1e-117       1     335 [.      10     335 ..      10     337 .] 0.97

  Alignments for each domain:
  == domain 1  score: 379.0 bits;  conditional E-value: 1e-117
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               +vaivGatGavG+e+++vL+ r+fp+ +l l+asersaG+ v+    e ++ + + e+ +g di l + 
  lcl|FitnessBrowser__azobra:AZOBR_RS14735  10 RVAIVGATGAVGREMVDVLHRRSFPVAELGLFASERSAGRTVETPFGEKTLVAFDVEKVKGYDIVLLAV 78 
                                               69****************************************998888899999999************ PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                                g  +ke ap +a+ g++viDn+safr d++vPL+vpe+na+ + +ak   +ianPnC+t  +vv+L p
  lcl|FitnessBrowser__azobra:AZOBR_RS14735  79 SGDFAKEHAPAIAAGGALVIDNSSAFRYDDNVPLIVPEINAHAMGDAK---LIANPNCTTAIAVVALGP 144
                                               **********************************************99...****************** PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               l+++++lkrv+vstYqa sGaG++g++eL++qt+  l+gk           + f ++i fn+ip+id +
  lcl|FitnessBrowser__azobra:AZOBR_RS14735 145 LHKAFGLKRVIVSTYQATSGAGAEGMAELEEQTRNQLDGKPVV-------NSVFRHPIPFNLIPQIDAF 206
                                               **********************************999887544.......689**************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                               +e+Gytkee+k+++etrkil+i+dl+vs t+vr+P +++hse++++e+  +++++ ++ +L +apgvvv
  lcl|FitnessBrowser__azobra:AZOBR_RS14735 207 QENGYTKEEMKVTWETRKILEIPDLPVSCTAVRIPTYRAHSEAITVETLSPVTPDAARAVLADAPGVVV 275
                                               ********************************************************************* PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkD.lskekglalfvvaDnlrkGaalnavqiael 335
                                                d+p + +yp+Pl+a+g+ +v vgrir   ++ ++gl+lfv +D+l+kGaalnavqiael
  lcl|FitnessBrowser__azobra:AZOBR_RS14735 276 KDVPADGVYPMPLNATGQFDVEVGRIRTSlIFGDHGLDLFVCGDQLLKGAALNAVQIAEL 335
                                               *****************************567799***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (337 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.32
//
[ok]

This GapMind analysis is from Apr 09 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