Alignments for a candidate for asd in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Klebsiella variicola At-22

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_012968177.1 KVAR_RS12625 aspartate-semialdehyde dehydrogenase

Query= BRENDA::C5BB06
         (367 letters)



>NCBI__GCF_000025465.1:WP_012968177.1
          Length = 372

 Score =  418 bits (1075), Expect = e-121
 Identities = 207/370 (55%), Positives = 267/370 (72%), Gaps = 4/370 (1%)

Query: 1   MKNVGFIGWRGMVGSVLMQRMSEERDFDAIRPLFFSTSQHGQPAPTFGGHGGTLQDASDI 60
           MK VG +GWRGMVGSVL+QRM EE DFD I   FFSTS  G   P   G    L+DA+ +
Sbjct: 1   MKQVGIVGWRGMVGSVLLQRMIEENDFDDISAHFFSTSSVGGVGPVINGKSDILKDANSL 60

Query: 61  DALKALDIIITCQGGDYTHAVYPRLRAAGWQGYWIDAASALRMQDDAIIILDPVNRAVID 120
            AL  +DIIITCQGGDYT A+YP L   GWQGYWIDAASALRM + A IILDPVNR  ID
Sbjct: 61  SALAEMDIIITCQGGDYTKAIYPALINHGWQGYWIDAASALRMDEKACIILDPVNRDNID 120

Query: 121 RGLENGVKTFVGGNCTVSLMLMSLGGLFAADLVEWVSVATYQAASGGGARHMRELLTQMG 180
           R ++ GVK FVGGNC+++L LM L GL  ADL+EW+SV TYQ+ASG GA+ +REL+ Q  
Sbjct: 121 RAVKAGVKLFVGGNCSITLSLMGLAGLIKADLIEWMSVMTYQSASGAGAKQVRELIAQSA 180

Query: 181 MLHGQVAPALENPASAILDIERQVTDLMRNGTLPTDNFGVPLAGSLIPWIDKALDNGQSR 240
            +   ++      + ++L +  +V++L+ +  +P +NFGVPL GS+IPWID  L +G SR
Sbjct: 181 YISQHLSADELTASGSVLPLVNKVSELINSAGMPVENFGVPLMGSIIPWIDSDLGDGNSR 240

Query: 241 EEWKGQAETNKILA-SPQTIPIDGLCVRVGALRCHSQAFTVKLKRDIAIPEVEQLLARHN 299
           EEWKG+AETNKIL  +P TIP++GLC+RVG +RCHS A T+KLKR+++  E  +L+   +
Sbjct: 241 EEWKGEAETNKILGLAPGTIPVNGLCIRVGVIRCHSAAITLKLKREVSEAEFAELITHSH 300

Query: 300 EWVRVIPNDRELSMRELTPAAVTGTLATPVGRLRK--LNMGPQYLSAFTVGDQLLWGAAE 357
            WV  + N+++ S+ +LTPAA++G+L   +GR +K  LN  P Y S  TVGDQLLWGAAE
Sbjct: 301 PWVNYVRNNKQESVNQLTPAAISGSLQVGIGRYKKMSLNNEPVY-SVLTVGDQLLWGAAE 359

Query: 358 PLRRMLRLLL 367
           PLRRML +LL
Sbjct: 360 PLRRMLNILL 369


Lambda     K      H
   0.321    0.137    0.418 

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: 403
Number of extensions: 13
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_012968177.1 KVAR_RS12625 (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.2930659.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-159  514.3   0.7   9.4e-159  514.1   0.7    1.0  1  NCBI__GCF_000025465.1:WP_012968177.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012968177.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.1   0.7  9.4e-159  9.4e-159       1     366 []       2     369 ..       2     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 514.1 bits;  conditional E-value: 9.4e-159
                             TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqg 73 
                                           k+vg+vgwrgmvgsvll+rm ee+dfd i++ ffsts +g+ +p++++ s il+da+ + al e+diiitcqg
  NCBI__GCF_000025465.1:WP_012968177.1   2 KQVGIVGWRGMVGSVLLQRMIEENDFDDISAHFFSTSSVGGVGPVINGKSDILKDANSLSALAEMDIIITCQG 74 
                                           68*********************************************************************** PP

                             TIGR01745  74 gdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslggl 146
                                           gdytk iyp l + gw+gywidaas+lrm++ a iildpvn d i+ av+ g++ fvggnc+++l lm+l gl
  NCBI__GCF_000025465.1:WP_012968177.1  75 GDYTKAIYPALINHGWQGYWIDAASALRMDEKACIILDPVNRDNIDRAVKAGVKLFVGGNCSITLSLMGLAGL 147
                                           ************************************************************************* PP

                             TIGR01745 147 frdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsv 219
                                           ++ +l+ew+sv+tyq+asg+ga+ +rel+ q   + +++  + +++s ++l + +kv++l+ s  +pvenf+v
  NCBI__GCF_000025465.1:WP_012968177.1 148 IKADLIEWMSVMTYQSASGAGAKQVRELIAQSAYISQHLSADELTASGSVLPLVNKVSELINSAGMPVENFGV 220
                                           ************************************************************************* PP

                             TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilgtk.dtilvdglcvrigalrchsqaltiklkkdvsleeie 291
                                           pl gs+ipwid +l +g+sreewkg+aetnkilg +  ti+v+glc+r+g +rchs a+t+klk++vs  e  
  NCBI__GCF_000025465.1:WP_012968177.1 221 PLMGSIIPWIDSDLGDGNSREEWKGEAETNKILGLApGTIPVNGLCIRVGVIRCHSAAITLKLKREVSEAEFA 293
                                           **********************************87379********************************** PP

                             TIGR01745 292 eiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeyl.saftvgdqllwgaaeplrrmlr 363
                                           e+i+   +wv++v n+++ ++++ltpaa++g+l++++gr +k+ + +e + s +tvgdqllwgaaeplrrml+
  NCBI__GCF_000025465.1:WP_012968177.1 294 ELITHSHPWVNYVRNNKQESVNQLTPAAISGSLQVGIGRYKKMSLNNEPVySVLTVGDQLLWGAAEPLRRMLN 366
                                           *******************************************99988553999******************* PP

                             TIGR01745 364 ill 366
                                           ill
  NCBI__GCF_000025465.1:WP_012968177.1 367 ILL 369
                                           *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (372 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: 00:00:00.00
# Mc/sec: 22.78
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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