Alignments for a candidate for dapC in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Persephonella marina EX-H1

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_012675382.1 PERMA_RS03815 succinyldiaminopimelate transaminase

Query= BRENDA::Q82IK5
         (364 letters)



>NCBI__GCF_000021565.1:WP_012675382.1
          Length = 391

 Score =  160 bits (406), Expect = 4e-44
 Identities = 118/381 (30%), Positives = 175/381 (45%), Gaps = 35/381 (9%)

Query: 8   LPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALV-AAADSPGYPTVWGTP 66
           L  +P ++L   KA        I D   G P +P    I++AL+ A  +   YP+V G  
Sbjct: 8   LKPYPMEELNRIKAELKDKGIKIYDFGTGDPKEPTDPKIRQALIDAVPEVSQYPSVAGRK 67

Query: 67  ELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPT---QLGLGPGDKVAHPRLAYP 123
           ELR+A++ W   R G +      ++P  GSKE +   P       +   +KV     AYP
Sbjct: 68  ELREAVSRWFLNRFGVKLDPDSQIIPSNGSKEAIFHFPLVFIDTDIPEKNKVIFGTPAYP 127

Query: 124 TYEVGARLARADHVVYD--------------DPTELDPTGLKLLWLNSPSNPTGKVLSKA 169
            YE G   A    V                 D + L+ T  K++W+N P NPTG    ++
Sbjct: 128 VYERGTLYAGGVPVPVPLREEDGFLLRLDKLDKSLLEET--KIVWINYPHNPTGATAPRS 185

Query: 170 ELTRIVAWAREHGILVFSDECYLELGWEADPVSVLHPDVCGGSYEGIVSVHSLSKRSNLA 229
               +    R++GI++ SDECY E+ +   P+S L   +     EG+V  HSLSKRS L 
Sbjct: 186 YFEEVYGICRDYGIILCSDECYTEIYYGEKPLSALQTGI-----EGVVVFHSLSKRSGLT 240

Query: 230 GYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAARRTAL 289
           GYR  F+AGDP ++    + R   G+ T    Q A   A  D+ HV E+R+ +  +R   
Sbjct: 241 GYRTGFIAGDPNLIKEYRKGRASFGVATPDFIQKAAEVAWSDEEHVEERRKIFNEKRKIF 300

Query: 290 RDALLSHGFRIEHSEASLYLW--ATRGESCWDTVAHLADLGILVAPGDFYGSAGE----- 342
            +     G +  + EA+ Y W  A  G +  +   HL   GI+V+PG  + S  E     
Sbjct: 301 IEFFDRIGLKYLYPEATFYFWIKAPDGMTGEEYAKHLLKYGIVVSPGVNFCSGIEILENR 360

Query: 343 ---QFVRVALTATDERVAAAV 360
              ++ R+AL  T E    AV
Sbjct: 361 CSSEYFRIALVPTVEECREAV 381


Lambda     K      H
   0.319    0.135    0.420 

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: 422
Number of extensions: 23
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: 364
Length of database: 391
Length adjustment: 30
Effective length of query: 334
Effective length of database: 361
Effective search space:   120574
Effective search space used:   120574
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_012675382.1 PERMA_RS03815 (succinyldiaminopimelate transaminase)
to HMM TIGR03537 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

# 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/TIGR03537.hmm
# target sequence database:        /tmp/gapView.24413.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03537  [M=350]
Accession:   TIGR03537
Description: DapC: succinyldiaminopimelate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-181  586.9   0.0     7e-181  586.7   0.0    1.0  1  lcl|NCBI__GCF_000021565.1:WP_012675382.1  PERMA_RS03815 succinyldiaminopim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012675382.1  PERMA_RS03815 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.7   0.0    7e-181    7e-181       1     349 [.      29     386 ..      29     387 .. 0.99

  Alignments for each domain:
  == domain 1  score: 586.7 bits;  conditional E-value: 7e-181
                                 TIGR03537   1 rlydfGtGdpkeptddfirkalldavpevsqypsvlGekalreaiagylerrfgvkldpdaevlpsaGs 69 
                                               ++ydfGtGdpkeptd+ ir+al+davpevsqypsv+G+k+lrea+++++  rfgvkldpd++++ps Gs
  lcl|NCBI__GCF_000021565.1:WP_012675382.1  29 KIYDFGTGDPKEPTDPKIRQALIDAVPEVSQYPSVAGRKELREAVSRWFLNRFGVKLDPDSQIIPSNGS 97 
                                               79******************************************************************* PP

                                 TIGR03537  70 keaifhlplafldpe.eerkkviygtpgypvyerGalfaggealkvklkkedgflleldaveeailret 137
                                               keaifh+pl+f+d + +e++kvi+gtp+ypvyerG+l+agg +++v l++edgfll+ld++++++l+et
  lcl|NCBI__GCF_000021565.1:WP_012675382.1  98 KEAIFHFPLVFIDTDiPEKNKVIFGTPAYPVYERGTLYAGGVPVPVPLREEDGFLLRLDKLDKSLLEET 166
                                               *************98457889************************************************ PP

                                 TIGR03537 138 kivwinyphnptGaeapasylkevaelareygiilasdecyaeiyseekpasvlevglenvlafhslsk 206
                                               kivwinyphnptGa+ap+sy++ev  ++r+ygiil+sdecy+eiy +ekp s+l+ g+e v++fhslsk
  lcl|NCBI__GCF_000021565.1:WP_012675382.1 167 KIVWINYPHNPTGATAPRSYFEEVYGICRDYGIILCSDECYTEIYYGEKPLSALQTGIEGVVVFHSLSK 235
                                               ********************************************************************* PP

                                 TIGR03537 207 rsGmtGyrsgflaGdeelvsalrklrasvGvaspefvqaaataawsddahvaerrkifkrkrdlflefl 275
                                               rsG+tGyr+gf+aGd++l++ +rk ras+Gva+p+f+q+aa+ awsd++hv+errkif++kr++f+ef+
  lcl|NCBI__GCF_000021565.1:WP_012675382.1 236 RSGLTGYRTGFIAGDPNLIKEYRKGRASFGVATPDFIQKAAEVAWSDEEHVEERRKIFNEKRKIFIEFF 304
                                               ********************************************************************* PP

                                 TIGR03537 276 akkGlealasdatfylwvkvpegidaksyalrlleeGivvapGeafgag........eeeyvrvalvpt 336
                                                + Gl++l+++atfy+w+k+p+g+++++ya++ll+ Givv+pG +f++g        ++ey+r+alvpt
  lcl|NCBI__GCF_000021565.1:WP_012675382.1 305 DRIGLKYLYPEATFYFWIKAPDGMTGEEYAKHLLKYGIVVSPGVNFCSGieilenrcSSEYFRIALVPT 373
                                               ********************************************************************* PP

                                 TIGR03537 337 leeceeairlwer 349
                                               +eec+ea+++we+
  lcl|NCBI__GCF_000021565.1:WP_012675382.1 374 VEECREAVSVWEK 386
                                               ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (350 nodes)
Target sequences:                          1  (391 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: 10.58
//
[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