Alignments for a candidate for asd in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Polaromonas naphthalenivorans CJ2

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011802413.1 PNAP_RS15215 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000015505.1:WP_011802413.1
          Length = 379

 Score =  495 bits (1274), Expect = e-145
 Identities = 246/370 (66%), Positives = 289/370 (78%), Gaps = 5/370 (1%)

Query: 5   GLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDELK 64
           GL+GWRGMVGSVL+ RM  E DF+LIEPVFF+TSN GG+ P   ++   LKDA+ I+ LK
Sbjct: 9   GLVGWRGMVGSVLIDRMQAEGDFELIEPVFFSTSNAGGKAPAQARNETTLKDAFDIEALK 68

Query: 65  TLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQALD 124
             D+ILT QGGDYT+EVFPKLR AGW G+WIDAAS+LRM DDAVIVLDPVN  VI  AL 
Sbjct: 69  KCDIILTAQGGDYTAEVFPKLRAAGWTGHWIDAASTLRMNDDAVIVLDPVNLPVIKNALT 128

Query: 125 AGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAHA 184
            G  N++GGNCTVS MLM +G L+ AGLVEWM++MTYQAASG GAQ+MRELL Q G  ++
Sbjct: 129 KGGNNWVGGNCTVSCMLMGVGALYKAGLVEWMTSMTYQAASGGGAQHMRELLTQFGTLNS 188

Query: 185 SVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243
            V   L +P SAIL+IDR++    +S  A  T +FG PLGGSLIPWIDK+L +G S+EEW
Sbjct: 189 EVKSLLDDPKSAILEIDRRILAKQQSLSALETANFGVPLGGSLIPWIDKDLGDGMSKEEW 248

Query: 244 KAQAETNKILARFKN----PIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299
           K  AETNKIL +  +      PVDG CVR+GAMRCHSQALT KL KDVPL DIE +I+  
Sbjct: 249 KGGAETNKILGQGASFGTAETPVDGFCVRIGAMRCHSQALTFKLKKDVPLADIEAMIAAD 308

Query: 300 NPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEP 359
           N WVK++PN RE S+R+LTP AVTGT+ +PVGRLRKL MG  YLGAFTVGDQLLWGAAEP
Sbjct: 309 NAWVKVIPNTREASIRDLTPVAVTGTMQIPVGRLRKLAMGPDYLGAFTVGDQLLWGAAEP 368

Query: 360 LRRMLRILLE 369
           LRRMLRIL+E
Sbjct: 369 LRRMLRILIE 378


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: 533
Number of extensions: 20
Number of successful extensions: 3
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: 379
Length adjustment: 30
Effective length of query: 340
Effective length of database: 349
Effective search space:   118660
Effective search space used:   118660
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 WP_011802413.1 PNAP_RS15215 (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.704.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-180  585.8   0.1   1.8e-180  585.6   0.1    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011802413.1  PNAP_RS15215 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802413.1  PNAP_RS15215 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.6   0.1  1.8e-180  1.8e-180       3     366 .]       8     377 ..       6     377 .. 0.96

  Alignments for each domain:
  == domain 1  score: 585.6 bits;  conditional E-value: 1.8e-180
                                 TIGR01745   3 vglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitc 71 
                                                glvgwrgmvgsvl++rmq e df++i+pvffsts++g+kap+ a+ +++l+da+di+alk++dii+t 
  lcl|NCBI__GCF_000015505.1:WP_011802413.1   8 TGLVGWRGMVGSVLIDRMQAEGDFELIEPVFFSTSNAGGKAPAQARNETTLKDAFDIEALKKCDIILTA 76 
                                               69******************************************************************* PP

                                 TIGR01745  72 qggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslll 140
                                               qggdyt e++pklr+agw g+widaas+lrm+ddavi+ldpvnl vik+a++kg +++vggnctvs +l
  lcl|NCBI__GCF_000015505.1:WP_011802413.1  77 QGGDYTAEVFPKLRAAGWTGHWIDAASTLRMNDDAVIVLDPVNLPVIKNALTKGGNNWVGGNCTVSCML 145
                                               ********************************************************************* PP

                                 TIGR01745 141 mslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrs 209
                                               m++g l++ +lvew++++tyqaasggga+hmrell+q+g+l  ev++ l  p sailei+r++    +s
  lcl|NCBI__GCF_000015505.1:WP_011802413.1 146 MGVGALYKAGLVEWMTSMTYQAASGGGAQHMRELLTQFGTLNSEVKSLLDDPKSAILEIDRRILAKQQS 214
                                               *************************************************************98665555 PP

                                 TIGR01745 210 .eelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgt.....kdtilvdglcvrigalrc 272
                                                + l + nf+vpl gslipwidk+l +g s+eewkg aetnkilg      +   +vdg cvriga+rc
  lcl|NCBI__GCF_000015505.1:WP_011802413.1 215 lSALETANFGVPLGGSLIPWIDKDLGDGMSKEEWKGGAETNKILGQgasfgTAETPVDGFCVRIGAMRC 283
                                               2789****************************************862111123469************* PP

                                 TIGR01745 273 hsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeyl 341
                                               hsqalt+klkkdv+l +ie +i+a+n wvkv+pn re ++r+ltp avtgt++ipvgrlrkl mg++yl
  lcl|NCBI__GCF_000015505.1:WP_011802413.1 284 HSQALTFKLKKDVPLADIEAMIAADNAWVKVIPNTREASIRDLTPVAVTGTMQIPVGRLRKLAMGPDYL 352
                                               ********************************************************************* PP

                                 TIGR01745 342 saftvgdqllwgaaeplrrmlrill 366
                                                aftvgdqllwgaaeplrrmlril+
  lcl|NCBI__GCF_000015505.1:WP_011802413.1 353 GAFTVGDQLLWGAAEPLRRMLRILI 377
                                               ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (379 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: 11.00
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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