Alignments for a candidate for asd in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Marinobacter adhaerens HP15

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate GFF1874 HP15_1831 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__Marino:GFF1874
          Length = 360

 Score =  521 bits (1343), Expect = e-153
 Identities = 252/360 (70%), Positives = 302/360 (83%), Gaps = 1/360 (0%)

Query: 12  MVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKD-IAPLKDAYSIDELKTLDVIL 70
           MVGSVLMQRM EE DF  IEPVFFTTS  G   P+VGKD + PL+DA+ ++ LKT+DVI+
Sbjct: 1   MVGSVLMQRMREENDFADIEPVFFTTSQAGKPAPDVGKDDVPPLQDAFDVEILKTMDVIV 60

Query: 71  TCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQALDAGTRNY 130
           TCQGGDYT  V+ KLR+AGW+GYWIDAAS+LRM D +VIVLDPVNR VID AL+ G ++Y
Sbjct: 61  TCQGGDYTGAVYQKLRDAGWEGYWIDAASTLRMVDHSVIVLDPVNRNVIDAALEKGVKDY 120

Query: 131 IGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAHASVADDL 190
           IGGNCTVSLM++ALGGL +  L+EW+S MTYQAASG+GAQNMRELL QMG  + SV  +L
Sbjct: 121 IGGNCTVSLMMLALGGLLEQDLIEWVSPMTYQAASGSGAQNMRELLNQMGELNKSVKSEL 180

Query: 191 ANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEWKAQAETN 250
            +P+SAIL+IDRKV ET+RS+ FPTEHF  PL GSLIP+IDK+L NG S+EEWKA  ETN
Sbjct: 181 DDPSSAILEIDRKVTETMRSDGFPTEHFQVPLAGSLIPFIDKQLDNGMSKEEWKAGVETN 240

Query: 251 KILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNPWVKLVPNHR 310
           KIL R  NPIP+DGICVR+GAMR HSQALTIKL KD+P+++IE ++++ N WVK++PN R
Sbjct: 241 KILGRSDNPIPIDGICVRIGAMRSHSQALTIKLKKDLPVSEIESILAKANDWVKVIPNDR 300

Query: 311 EVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRRMLRILLER 370
           + ++ ELTPA VTGTLSVPVGR+RKL MG +Y+ AFTVGDQLLWGAAEPLRRMLRIL ER
Sbjct: 301 DATIEELTPAKVTGTLSVPVGRIRKLTMGPEYISAFTVGDQLLWGAAEPLRRMLRILQER 360


Lambda     K      H
   0.319    0.136    0.409 

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: 494
Number of extensions: 10
Number of successful extensions: 2
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: 370
Length of database: 360
Length adjustment: 30
Effective length of query: 340
Effective length of database: 330
Effective search space:   112200
Effective search space used:   112200
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 GFF1874 HP15_1831 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (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/TIGR01745.hmm
# target sequence database:        /tmp/gapView.3556661.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01745  [M=366]
Accession:   TIGR01745
Description: asd_gamma: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.1e-184  597.0   0.0   6.8e-184  596.8   0.0    1.0  1  FitnessBrowser__Marino:GFF1874  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF1874  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.8   0.0  6.8e-184  6.8e-184      11     365 ..       1     357 [.       1     358 [. 0.99

  Alignments for each domain:
  == domain 1  score: 596.8 bits;  conditional E-value: 6.8e-184
                       TIGR01745  11 mvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa.iledaydidalkeldiiitcqggdytkeiypklrkag 88 
                                     mvgsvl++rm+ee+df  i+pvff+tsq+g+ ap ++k +  +l+da+d+++lk +d+i+tcqggdyt  +y klr+ag
  FitnessBrowser__Marino:GFF1874   1 MVGSVLMQRMREENDFADIEPVFFTTSQAGKPAPDVGKDDVpPLQDAFDVEILKTMDVIVTCQGGDYTGAVYQKLRDAG 79 
                                     9***************************************989************************************ PP

                       TIGR01745  89 wkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrdelvewvsvatyqaasggg 167
                                     w+gywidaas+lrm d +vi+ldpvn +vi+ a++kg+++++ggnctvsl++++lggl++++l+ewvs +tyqaasg+g
  FitnessBrowser__Marino:GFF1874  80 WEGYWIDAASTLRMVDHSVIVLDPVNRNVIDAALEKGVKDYIGGNCTVSLMMLALGGLLEQDLIEWVSPMTYQAASGSG 158
                                     ******************************************************************************* PP

                       TIGR01745 168 arhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplagslipwidkqldngqsreewkgqa 246
                                     a+ mrell+qmg l k+v++el  pssailei+rkvt+++rs+ +p+e+f+vplagslip+idkqldng s+eewk   
  FitnessBrowser__Marino:GFF1874 159 AQNMRELLNQMGELNKSVKSELDDPSSAILEIDRKVTETMRSDGFPTEHFQVPLAGSLIPFIDKQLDNGMSKEEWKAGV 237
                                     ******************************************************************************* PP

                       TIGR01745 247 etnkilgtkd.tilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtl 324
                                     etnkilg +d  i++dg+cvriga+r hsqaltiklkkd+++ eie+i+++ n+wvkv+pn+r+ t++eltpa vtgtl
  FitnessBrowser__Marino:GFF1874 238 ETNKILGRSDnPIPIDGICVRIGAMRSHSQALTIKLKKDLPVSEIESILAKANDWVKVIPNDRDATIEELTPAKVTGTL 316
                                     *******87626******************************************************************* PP

                       TIGR01745 325 dipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365
                                     ++pvgr+rkl mg+ey+saftvgdqllwgaaeplrrmlril
  FitnessBrowser__Marino:GFF1874 317 SVPVGRIRKLTMGPEYISAFTVGDQLLWGAAEPLRRMLRIL 357
                                     ***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (360 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: 15.60
//
[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