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.626934.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 18.44
//
[ok]

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

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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:

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:

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:

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:

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