Alignments for a candidate for asd in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Pseudarthrobacter sulfonivorans Ar51

Align aspartate-semialdehyde dehydrogenase (characterized)
to candidate WP_058931682.1 AU252_RS16600 aspartate-semialdehyde dehydrogenase

Query= CharProtDB::CH_024631
         (367 letters)



>NCBI__GCF_001484605.1:WP_058931682.1
          Length = 380

 Score =  465 bits (1197), Expect = e-136
 Identities = 234/367 (63%), Positives = 280/367 (76%), Gaps = 7/367 (1%)

Query: 3   NVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTT----GTLQDAF 58
           +VG +GWRGMVGSVLMQRM +E DF  I PVFFSTS  G AAPS  G      G L+DAF
Sbjct: 8   SVGLVGWRGMVGSVLMQRMQDEGDFANINPVFFSTSNAGGAAPSIAGAAAGAAGKLEDAF 67

Query: 59  DLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDV 118
           D++ L  L IIVT QGGDYT  ++ +LR  GW G WIDAAS+LRM DD+II+LDP+N+DV
Sbjct: 68  DVDTLAKLPIIVTAQGGDYTKRVHTELRGRGWDGLWIDAASTLRMNDDSIIVLDPINRDV 127

Query: 119 ITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQ 178
           I  GL NG + F+GGNCTVS MLM LGGLF N LV+W +  TYQAASGGGARHMRELL+Q
Sbjct: 128 IDKGLVNGTKDFIGGNCTVSCMLMGLGGLFKNGLVEWGTSMTYQAASGGGARHMRELLSQ 187

Query: 179 MGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQ 238
            G L   V+ EL  P+SAIL+I+RKV    RS ++    FGVPLAGSLIPWID  L NGQ
Sbjct: 188 FGTLNAEVSSELDDPASAILEIDRKVLAHQRS-DIDATQFGVPLAGSLIPWIDADLGNGQ 246

Query: 239 SREEWKGQAETNKILNTS--SVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLA 296
           S+EEWK   ETNKIL TS  + I +DGLC+R+GA+R HSQA T+KL++D+S+  +E+LLA
Sbjct: 247 SKEEWKAGVETNKILGTSDENRIIMDGLCIRIGAMRSHSQALTLKLREDLSVAEIEKLLA 306

Query: 297 AHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAA 356
             N WAKV+PN +E +M  LTP A +GTL  PVGR+RK+ MGPE++SAFTVGDQLLWGAA
Sbjct: 307 DDNEWAKVIPNTKEDSMAGLTPVAASGTLDIPVGRIRKMEMGPEYISAFTVGDQLLWGAA 366

Query: 357 EPLRRML 363
           EPLRRML
Sbjct: 367 EPLRRML 373


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: 482
Number of extensions: 13
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: 367
Length of database: 380
Length adjustment: 30
Effective length of query: 337
Effective length of database: 350
Effective search space:   117950
Effective search space used:   117950
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_058931682.1 AU252_RS16600 (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.22436.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-177  576.6   0.2   1.1e-177  576.4   0.2    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058931682.1  AU252_RS16600 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058931682.1  AU252_RS16600 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.4   0.2  1.1e-177  1.1e-177       2     364 ..       8     375 ..       7     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: 576.4 bits;  conditional E-value: 1.1e-177
                                 TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa....iledaydidalkeld 66 
                                                vglvgwrgmvgsvl++rmq+e df  i+pvffsts++g++aps+a+ +a     leda+d+d+l +l 
  lcl|NCBI__GCF_001484605.1:WP_058931682.1   8 SVGLVGWRGMVGSVLMQRMQDEGDFANINPVFFSTSNAGGAAPSIAGAAAgaagKLEDAFDVDTLAKLP 76 
                                               59*******************************************9765433448************** PP

                                 TIGR01745  67 iiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnct 135
                                               ii+t qggdytk ++ +lr  gw+g widaas+lrm+dd++i+ldp+n dvi+ ++ +g+++f+ggnct
  lcl|NCBI__GCF_001484605.1:WP_058931682.1  77 IIVTAQGGDYTKRVHTELRGRGWDGLWIDAASTLRMNDDSIIVLDPINRDVIDKGLVNGTKDFIGGNCT 145
                                               ********************************************************************* PP

                                 TIGR01745 136 vslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvt 204
                                               vs +lm+lgglf+++lvew +++tyqaasgggarhmrell+q+g+l  ev +el  p+sailei+rkv 
  lcl|NCBI__GCF_001484605.1:WP_058931682.1 146 VSCMLMGLGGLFKNGLVEWGTSMTYQAASGGGARHMRELLSQFGTLNAEVSSELDDPASAILEIDRKVL 214
                                               ********************************************************************* PP

                                 TIGR01745 205 klsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkd..tilvdglcvrigalr 271
                                                  r +++ + +f+vplagslipwid +l ngqs+eewk   etnkilgt+d   i +dglc+riga+r
  lcl|NCBI__GCF_001484605.1:WP_058931682.1 215 AHQR-SDIDATQFGVPLAGSLIPWIDADLGNGQSKEEWKAGVETNKILGTSDenRIIMDGLCIRIGAMR 282
                                               ****.79*******************************************8633699************ PP

                                 TIGR01745 272 chsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkey 340
                                                hsqalt+kl+ d+s+ eie++++++n+w+kv+pn +e+++  ltp a +gtldipvgr+rk++mg+ey
  lcl|NCBI__GCF_001484605.1:WP_058931682.1 283 SHSQALTLKLREDLSVAEIEKLLADDNEWAKVIPNTKEDSMAGLTPVAASGTLDIPVGRIRKMEMGPEY 351
                                               ********************************************************************* PP

                                 TIGR01745 341 lsaftvgdqllwgaaeplrrmlri 364
                                               +saftvgdqllwgaaeplrrml+i
  lcl|NCBI__GCF_001484605.1:WP_058931682.1 352 ISAFTVGDQLLWGAAEPLRRMLNI 375
                                               **********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (380 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: 9.96
//
[ok]

This GapMind analysis is from Apr 10 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