Alignments for a candidate for asd in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Acidovorax sp. GW101-3H11

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate Ac3H11_1530 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1530
          Length = 385

 Score =  485 bits (1249), Expect = e-142
 Identities = 246/382 (64%), Positives = 295/382 (77%), Gaps = 14/382 (3%)

Query: 2   KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61
           K VGL+GWRGMVGSVLM RM +E+DFDLIEP+FF+TSN GG+ P   K+   L+DA++I+
Sbjct: 3   KLVGLVGWRGMVGSVLMDRMEQEKDFDLIEPMFFSTSNAGGKAPAQAKNETALQDAFNIE 62

Query: 62  ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121
            LK  ++I+T QGGDYTSEV+PKLR AGW G+WIDAASSLRME +AVIVLDPVN  VI  
Sbjct: 63  ALKRCEIIITAQGGDYTSEVYPKLRAAGWNGHWIDAASSLRMEKNAVIVLDPVNMPVIKN 122

Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181
           AL  G +++IGGNCTVS MLM +G L+ AGLVEWMS  TYQAASG GAQ+MRELL Q G 
Sbjct: 123 ALANGGKDWIGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGT 182

Query: 182 AHASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKEL------ 234
            +A V   L +P SAIL+IDRKV    R+     T +FG PLGGSLIPWIDK+L      
Sbjct: 183 LNAEVRSLLDDPKSAILEIDRKVIAKQRALTGAETANFGVPLGGSLIPWIDKDLGIGKSQ 242

Query: 235 --PN-GQSREEWKAQAETNKILARFKN----PIPVDGICVRVGAMRCHSQALTIKLNKDV 287
             P  G S+EEWK  AETNKIL + +      IPVDG CVRVGAMRCHSQALT KL KDV
Sbjct: 243 DEPGWGMSKEEWKGMAETNKILGQGEGFSTAAIPVDGFCVRVGAMRCHSQALTFKLKKDV 302

Query: 288 PLTDIEGLISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFT 347
           P+ DIE +++  N WVK+VPN RE ++++LTP AVTGT+++PVGR+RKL MG +Y+GAFT
Sbjct: 303 PVADIEAMVAADNEWVKVVPNTREATIQDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFT 362

Query: 348 VGDQLLWGAAEPLRRMLRILLE 369
           +GDQLLWGAAEPLRRMLRILL+
Sbjct: 363 IGDQLLWGAAEPLRRMLRILLD 384


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: 528
Number of extensions: 18
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: 385
Length adjustment: 30
Effective length of query: 340
Effective length of database: 355
Effective search space:   120700
Effective search space used:   120700
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 Ac3H11_1530 (Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
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.3316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.5e-179  581.9   0.3     4e-179  581.2   0.3    1.3  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530  Aspartate-semialdehyde dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530  Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.2   0.3    4e-179    4e-179       2     366 .]       4     383 ..       3     383 .. 0.95

  Alignments for each domain:
  == domain 1  score: 581.2 bits;  conditional E-value: 4e-179
                                        TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalk 63 
                                                       vglvgwrgmvgsvl++rm++ekdfd+i+p+ffsts++g+kap+ ak +++l+da++i+alk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530   4 LVGLVGWRGMVGSVLMDRMEQEKDFDLIEPMFFSTSNAGGKAPAQAKNETALQDAFNIEALK 65 
                                                      69************************************************************ PP

                                        TIGR01745  64 eldiiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkg 125
                                                      +++iiit qggdyt+e+ypklr+agw+g+widaasslrm+++avi+ldpvn+ vik+a+++g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530  66 RCEIIITAQGGDYTSEVYPKLRAAGWNGHWIDAASSLRMEKNAVIVLDPVNMPVIKNALANG 127
                                                      ************************************************************** PP

                                        TIGR01745 126 irtfvggnctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykevee 187
                                                       ++++ggnctvs +lm++g l++ +lvew+s++tyqaasggga+hmrell+q g+l  ev +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 128 GKDWIGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGTLNAEVRS 189
                                                      ************************************************************** PP

                                        TIGR01745 188 elakpssaileierkvtklsrs.eelpvenfsvplagslipwidkqldngq.........sr 239
                                                       l  p sailei+rkv    r+ +   + nf+vpl gslipwidk+l  g+         s+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 190 LLDDPKSAILEIDRKVIAKQRAlTGAETANFGVPLGGSLIPWIDKDLGIGKsqdepgwgmSK 251
                                                      ****************999997356889******************9765422222222279 PP

                                        TIGR01745 240 eewkgqaetnkilg.....tkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiira 296
                                                      eewkg aetnkilg     ++ +i+vdg cvr+ga+rchsqalt+klkkdv++ +ie +++a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 252 EEWKGMAETNKILGqgegfSTAAIPVDGFCVRVGAMRCHSQALTFKLKKDVPVADIEAMVAA 313
                                                      9************9333333568*************************************** PP

                                        TIGR01745 297 hnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaepl 358
                                                      +n+wvkvvpn re t+++ltp avtgt++ipvgr+rkl mg+ey+ aft+gdqllwgaaepl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 314 DNEWVKVVPNTREATIQDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTIGDQLLWGAAEPL 375
                                                      ************************************************************** PP

                                        TIGR01745 359 rrmlrill 366
                                                      rrmlrill
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 376 RRMLRILL 383
                                                      ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (385 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 3.35
//
[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