Alignments for a candidate for asd in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Sphingomonas wittichii RW1

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_012048872.1 SWIT_RS13495 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_000016765.1:WP_012048872.1
          Length = 341

 Score =  337 bits (864), Expect = 3e-97
 Identities = 181/335 (54%), Positives = 233/335 (69%), Gaps = 7/335 (2%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFN--GKTVRVQNVEEF 62
           + V + GATG VG  ML +L EREFP+ EL  +AS RS+G    F   GK ++VQN+E F
Sbjct: 3   YRVVVAGATGNVGREMLNILAEREFPIAELAAVASARSQGDQIEFGETGKMLKVQNIEHF 62

Query: 63  DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122
           DWS   IALF+ G + +  +APIAA AG  VIDN+S +R D D+PL+VPEVNPEAI  ++
Sbjct: 63  DWSGWDIALFAIGSDATKIYAPIAAAAGCTVIDNSSLYRMDPDVPLIVPEVNPEAIDGYK 122

Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182
            RNIIANPNCST QM+VALKP++DA  I+R+ V+TYQSVSGAGKAG+DEL  Q+  +  G
Sbjct: 123 VRNIIANPNCSTAQMVVALKPLHDAATIKRVVVSTYQSVSGAGKAGMDELFEQSRNIFVG 182

Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242
            PAE   F++QIAFN IP ID+F+D+G+TKEE KMV ET+KI  DP + V  TCVRVPVF
Sbjct: 183 DPAEPKKFTKQIAFNVIPHIDKFLDDGFTKEEWKMVVETKKIM-DPKVKVTATCVRVPVF 241

Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVR 299
            GH+EA+++E    + AE    +L +  G+ L        + T V +  G+    V RVR
Sbjct: 242 VGHSEAINIEFEKELSAEDAQKILREAPGVMLVDKREDGGYVTPV-ECVGEFATYVSRVR 300

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334
            D +  +G+ LW V+DN+RKGAA NAVQIAELL R
Sbjct: 301 EDPTVENGLVLWCVSDNLRKGAALNAVQIAELLGR 335


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: 356
Number of extensions: 15
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: 341
Length adjustment: 28
Effective length of query: 309
Effective length of database: 313
Effective search space:    96717
Effective search space used:    96717
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_012048872.1 SWIT_RS13495 (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.8214.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-141  456.9   0.1   2.4e-141  456.7   0.1    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012048872.1  SWIT_RS13495 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012048872.1  SWIT_RS13495 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.7   0.1  2.4e-141  2.4e-141       2     336 ..       5     333 ..       4     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 2.4e-141
                                 TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfk..gkeleveeaekesfegidialfs 68 
                                               v + GatG+vG+e+l++L+er+fpi +l ++as+rs+G +++f   gk l+v+++e+++ +g dialf+
  lcl|NCBI__GCF_000016765.1:WP_012048872.1   5 VVVAGATGNVGREMLNILAEREFPIAELAAVASARSQGDQIEFGetGKMLKVQNIEHFDWSGWDIALFA 73 
                                               7899***************************************633699******************** PP

                                 TIGR01296  69 aGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLk 137
                                                G+   k +ap aa+ag++viDn+s++r+d+dvPL+vpevn e +   k ++iianPnCst q+vv+Lk
  lcl|NCBI__GCF_000016765.1:WP_012048872.1  74 IGSDATKIYAPIAAAAGCTVIDNSSLYRMDPDVPLIVPEVNPEAIDGYKVRNIIANPNCSTAQMVVALK 142
                                               ********************************************************************* PP

                                 TIGR01296 138 plkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidk 206
                                               pl+d+a +krvvvstYq+vsGaGk+g++eL +q + +++g   ep       kkf+kqiafn+ip+idk
  lcl|NCBI__GCF_000016765.1:WP_012048872.1 143 PLHDAATIKRVVVSTYQSVSGAGKAGMDELFEQSRNIFVGDPAEP-------KKFTKQIAFNVIPHIDK 204
                                               **************************************9988886.......9**************** PP

                                 TIGR01296 207 lkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvv 275
                                               + +dG+tkee k++ et+ki++ +++kv+atcvrvPvf+ghse+++iefekels+e+++++L+eapgv+
  lcl|NCBI__GCF_000016765.1:WP_012048872.1 205 FLDDGFTKEEWKMVVETKKIMD-PKVKVTATCVRVPVFVGHSEAINIEFEKELSAEDAQKILREAPGVM 272
                                               **********************.********************************************** PP

                                 TIGR01296 276 viddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336
                                               ++d+ ++  y+tP+e vg+ +++v+r+r+D + e+gl l++v+DnlrkGaalnavqiaell
  lcl|NCBI__GCF_000016765.1:WP_012048872.1 273 LVDKREDGGYVTPVECVGEFATYVSRVREDPTVENGLVLWCVSDNLRKGAALNAVQIAELL 333
                                               ***********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (341 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: 10.48
//
[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