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.29550.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.77
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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