Alignments for a candidate for asd in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Allochromatium vinosum DSM 180

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_012970812.1 ALVIN_RS07955 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000025485.1:WP_012970812.1
          Length = 371

 Score =  552 bits (1422), Expect = e-162
 Identities = 271/371 (73%), Positives = 310/371 (83%), Gaps = 1/371 (0%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFD-LIEPVFFTTSNVGGQGPEVGKDIAPLKDAYS 59
           MKRVG +GWRGMVGSVLM+RM  E DF  L EPVFFTTS VG  GP+VG+  +PL DA S
Sbjct: 1   MKRVGFVGWRGMVGSVLMERMRAENDFARLAEPVFFTTSQVGQPGPDVGQGASPLLDAES 60

Query: 60  IDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVI 119
           +D L+ +D I+TCQGGDYT  + P+LR +GW GYWIDAASSLRME DA I+LDPVNR VI
Sbjct: 61  LDALREMDAIVTCQGGDYTKSIHPRLRASGWNGYWIDAASSLRMEPDATIILDPVNRPVI 120

Query: 120 DQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQM 179
           D ALD+G R++IGGNCTVSLMLMA+GGLF  GLVEW+SAMTYQAASGAGA+NMRELL QM
Sbjct: 121 DAALDSGKRDFIGGNCTVSLMLMAIGGLFREGLVEWVSAMTYQAASGAGAKNMRELLAQM 180

Query: 180 GAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQS 239
           GA H SV   LA+PASAILDIDR+V ETLR   FPTE FG PL GSLIPWID +L NGQS
Sbjct: 181 GALHGSVESLLADPASAILDIDRRVTETLRDPGFPTESFGVPLAGSLIPWIDTQLDNGQS 240

Query: 240 REEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299
           REEWK QAETN+IL R   PIPVDG+CVRVGAMRCHSQ LTIKLN+D+ L++IE LI+  
Sbjct: 241 REEWKGQAETNRILGRTDQPIPVDGLCVRVGAMRCHSQGLTIKLNRDIALSEIESLIASA 300

Query: 300 NPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEP 359
           N WV++VPN R V++R+L+PAAVTG+L VPVGRLR +NMGS+YL AFTVGDQLLWGAAEP
Sbjct: 301 NDWVRVVPNDRAVTMRDLSPAAVTGSLHVPVGRLRTMNMGSRYLSAFTVGDQLLWGAAEP 360

Query: 360 LRRMLRILLER 370
           LRRML ILL+R
Sbjct: 361 LRRMLMILLDR 371


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: 525
Number of extensions: 16
Number of successful extensions: 2
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: 371
Length adjustment: 30
Effective length of query: 340
Effective length of database: 341
Effective search space:   115940
Effective search space used:   115940
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: 49 (23.5 bits)

Align candidate WP_012970812.1 ALVIN_RS07955 (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.27433.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-191  621.6   0.0   2.4e-191  621.4   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970812.1  ALVIN_RS07955 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970812.1  ALVIN_RS07955 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.4   0.0  2.4e-191  2.4e-191       1     366 []       2     369 ..       2     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 621.4 bits;  conditional E-value: 2.4e-191
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdai.kpvffstsqlgqkapslakisailedaydidalkeldii 68 
                                               k+vg+vgwrgmvgsvl++rm+ e+df ++ +pvff+tsq+gq +p +++ +++l da  +dal+e+d i
  lcl|NCBI__GCF_000025485.1:WP_012970812.1   2 KRVGFVGWRGMVGSVLMERMRAENDFARLaEPVFFTTSQVGQPGPDVGQGASPLLDAESLDALREMDAI 70 
                                               68************************987479************************************* PP

                                 TIGR01745  69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137
                                               +tcqggdytk i+p+lr++gw+gywidaasslrm+ da iildpvn  vi+ a++ g r+f+ggnctvs
  lcl|NCBI__GCF_000025485.1:WP_012970812.1  71 VTCQGGDYTKSIHPRLRASGWNGYWIDAASSLRMEPDATIILDPVNRPVIDAALDSGKRDFIGGNCTVS 139
                                               ********************************************************************* PP

                                 TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206
                                               l+lm++gglfr++lvewvs++tyqaasg+ga+ mrell qmg l+++ve+ la p+sail+i+r+vt++
  lcl|NCBI__GCF_000025485.1:WP_012970812.1 140 LMLMAIGGLFREGLVEWVSAMTYQAASGAGAKNMRELLAQMGALHGSVESLLADPASAILDIDRRVTET 208
                                               ********************************************************************* PP

                                 TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilg.tkdtilvdglcvrigalrchs 274
                                                r   +p+e f+vplagslipwid+qldngqsreewkgqaetn+ilg t + i+vdglcvr+ga+rchs
  lcl|NCBI__GCF_000025485.1:WP_012970812.1 209 LRDPGFPTESFGVPLAGSLIPWIDTQLDNGQSREEWKGQAETNRILGrTDQPIPVDGLCVRVGAMRCHS 277
                                               **********************************************856788***************** PP

                                 TIGR01745 275 qaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsa 343
                                               q+ltikl++d++l eie++i++ n+wv+vvpn+r +t+r+l+paavtg+l++pvgrlr +nmg +ylsa
  lcl|NCBI__GCF_000025485.1:WP_012970812.1 278 QGLTIKLNRDIALSEIESLIASANDWVRVVPNDRAVTMRDLSPAAVTGSLHVPVGRLRTMNMGSRYLSA 346
                                               ********************************************************************* PP

                                 TIGR01745 344 ftvgdqllwgaaeplrrmlrill 366
                                               ftvgdqllwgaaeplrrml ill
  lcl|NCBI__GCF_000025485.1:WP_012970812.1 347 FTVGDQLLWGAAEPLRRMLMILL 369
                                               *******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (371 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: 9.53
//
[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