Alignments for a candidate for asd in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Dechlorosoma suillum PS

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate Dsui_3197 Dsui_3197 aspartate-semialdehyde dehydrogenase, gamma-proteobacterial

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__PS:Dsui_3197
          Length = 377

 Score =  535 bits (1377), Expect = e-156
 Identities = 266/376 (70%), Positives = 310/376 (82%), Gaps = 7/376 (1%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVG--KDIAPLKDAY 58
           MKRVGL+GWRGMVGSVLMQRM+EE DF  IEPV+F+TSN GG+ P  G  +  APL+DA 
Sbjct: 1   MKRVGLVGWRGMVGSVLMQRMVEEGDFAHIEPVYFSTSNAGGKAPVFGGKEAAAPLQDAI 60

Query: 59  SIDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKV 118
           S+D LKT D+I+TCQGGDYT EVFPKLR AGW G+WIDAAS+LRM DDAVI+LDPVN+ V
Sbjct: 61  SVDALKTCDIIITCQGGDYTKEVFPKLRAAGWNGHWIDAASALRMADDAVIILDPVNKNV 120

Query: 119 IDQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQ 178
           I  +L  G +N+IGGNCTVSLMLM LGGLF   L+EW ++MTYQAASGAGAQNMREL+ Q
Sbjct: 121 IQDSLAKGGKNWIGGNCTVSLMLMGLGGLFQNDLIEWATSMTYQAASGAGAQNMRELIAQ 180

Query: 179 MGAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHF-GAPLGGSLIPWIDKELPNG 237
           MG  HASVAD LA+P+SAIL+IDRKVAET+RS+AFP ++F   PL GSLIPWID  + NG
Sbjct: 181 MGTIHASVADLLADPSSAILEIDRKVAETIRSDAFPKKNFRNTPLAGSLIPWIDVPVENG 240

Query: 238 QSREEWKAQAETNKILA----RFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIE 293
           QS+EEWK  AE NKIL     R +  IP+DG+CVR+GAMRCHSQALTIKL KDVPL +I 
Sbjct: 241 QSKEEWKGGAECNKILGKPAFRSQGSIPIDGLCVRIGAMRCHSQALTIKLKKDVPLDEIS 300

Query: 294 GLISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLL 353
            ++++ N W K+VPN RE+S RELTPAAVTGTL+VPVGRL K+ MG +YL AFT GDQLL
Sbjct: 301 DMLAKANQWAKVVPNEREISERELTPAAVTGTLTVPVGRLHKMAMGPEYLAAFTCGDQLL 360

Query: 354 WGAAEPLRRMLRILLE 369
           WGAAEPLRRMLRILLE
Sbjct: 361 WGAAEPLRRMLRILLE 376


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: 536
Number of extensions: 10
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: 370
Length of database: 377
Length adjustment: 30
Effective length of query: 340
Effective length of database: 347
Effective search space:   117980
Effective search space used:   117980
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: 50 (23.9 bits)

Align candidate Dsui_3197 Dsui_3197 (aspartate-semialdehyde dehydrogenase, gamma-proteobacterial)
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.4923.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-194  631.4   0.1   2.4e-194  631.2   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_3197  Dsui_3197 aspartate-semialdehyde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3197  Dsui_3197 aspartate-semialdehyde dehydrogenase, gamma-proteobacterial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  631.2   0.1  2.4e-194  2.4e-194       1     366 []       2     375 ..       2     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 631.2 bits;  conditional E-value: 2.4e-194
                         TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa..iledaydidalkeldiiitcqggd 75 
                                       k+vglvgwrgmvgsvl++rm+ee df +i+pv+fsts++g+kap++++ +a  +l+da  +dalk +diiitcqggd
  lcl|FitnessBrowser__PS:Dsui_3197   2 KRVGLVGWRGMVGSVLMQRMVEEGDFAHIEPVYFSTSNAGGKAPVFGGKEAaaPLQDAISVDALKTCDIIITCQGGD 78 
                                       68********************************************98765559*********************** PP

                         TIGR01745  76 ytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrdelv 152
                                       ytke++pklr+agw+g+widaas+lrm ddaviildpvn++vi+d+++kg ++++ggnctvsl+lm+lgglf+++l+
  lcl|FitnessBrowser__PS:Dsui_3197  79 YTKEVFPKLRAAGWNGHWIDAASALRMADDAVIILDPVNKNVIQDSLAKGGKNWIGGNCTVSLMLMGLGGLFQNDLI 155
                                       ***************************************************************************** PP

                         TIGR01745 153 ewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenf.svplagslipw 228
                                       ew +++tyqaasg+ga+ mrel+ qmg+++ +v++ la pssailei+rkv++++rs+ +p +nf ++plagslipw
  lcl|FitnessBrowser__PS:Dsui_3197 156 EWATSMTYQAASGAGAQNMRELIAQMGTIHASVADLLADPSSAILEIDRKVAETIRSDAFPKKNFrNTPLAGSLIPW 232
                                       *****************************************************************558********* PP

                         TIGR01745 229 idkqldngqsreewkgqaetnkilg.....tkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnkw 300
                                       id  ++ngqs+eewkg ae nkilg     ++  i++dglcvriga+rchsqaltiklkkdv+l+ei +++++ n+w
  lcl|FitnessBrowser__PS:Dsui_3197 233 IDVPVENGQSKEEWKGGAECNKILGkpafrSQGSIPIDGLCVRIGAMRCHSQALTIKLKKDVPLDEISDMLAKANQW 309
                                       ************************9333333568******************************************* PP

                         TIGR01745 301 vkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366
                                       +kvvpnerei++reltpaavtgtl++pvgrl k+ mg+eyl+aft gdqllwgaaeplrrmlrill
  lcl|FitnessBrowser__PS:Dsui_3197 310 AKVVPNEREISERELTPAAVTGTLTVPVGRLHKMAMGPEYLAAFTCGDQLLWGAAEPLRRMLRILL 375
                                       ****************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (377 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: 7.38
//
[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