Alignments for a candidate for dapC in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Halomonas desiderata SP1

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_086509348.1 BZY95_RS07615 succinyldiaminopimelate transaminase

Query= metacyc::MONOMER-6501
         (397 letters)



>NCBI__GCF_002151265.1:WP_086509348.1
          Length = 408

 Score =  369 bits (947), Expect = e-107
 Identities = 206/404 (50%), Positives = 248/404 (61%), Gaps = 13/404 (3%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP LDAL PYPFEKL  L A    P   L  I L+IGEP+HA  A     + A+    +
Sbjct: 1   MNPDLDALKPYPFEKLATLKAGVTPPAQ-LAHIPLTIGEPQHAPFAGALATLHAHQLDFA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGALV 120
            YP+T G P LR AI+ W  RR+ +   DPE +VLPV G+REA+FAF Q  +D S  A V
Sbjct: 60  RYPATSGIPELRGAIAAWARRRFRLDGLDPERQVLPVNGTREAIFAFVQAALDRSRPARV 119

Query: 121 VCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAG 180
             PNPFYQIYEGA LLAG  P+Y++      F      VP EVWR  Q++F+CSPGNP G
Sbjct: 120 AVPNPFYQIYEGATLLAGGQPHYLDCRAESGFRPDFDAVPAEVWREVQILFLCSPGNPTG 179

Query: 181 NVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVAF 240
            V    E++ L  L+D   F+IA+ ECYSE+YLDED PP G L+A   +GR  Y   + F
Sbjct: 180 AVTPRAEFQKLIALADEFDFIIASDECYSELYLDEDAPPPGLLEACAAMGRHDYRRCLVF 239

Query: 241 SSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRKTA 300
            SLSKRSN+PG+RSGFVAGDA L+A F  YRTYHG AMS  +  ASI AW+     R   
Sbjct: 240 HSLSKRSNLPGLRSGFVAGDAELIAPFKRYRTYHGCAMSLPLQHASITAWNDEAHVRANR 299

Query: 301 Q-YRAKFEAVLPILQNVLDVRAPQASFYLWAGTP-GSDTAFARELYGRTGVTVLPGSLLA 358
             YR KF AV  IL  VL+  AP+ASFYLW   P G D AF REL+    V+VLPGS + 
Sbjct: 300 DAYREKFAAVTEILAPVLEFPAPEASFYLWPAVPGGDDEAFTRELFAAEHVSVLPGSYMG 359

Query: 359 R----------EAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           R          +    NPG GRIR+ALVA L+  V+AA RI  F
Sbjct: 360 RPTTGDGRGRADGRGDNPGAGRIRLALVAELEPTVEAAGRIRRF 403


Lambda     K      H
   0.321    0.135    0.412 

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: 554
Number of extensions: 19
Number of successful extensions: 5
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: 397
Length of database: 408
Length adjustment: 31
Effective length of query: 366
Effective length of database: 377
Effective search space:   137982
Effective search space used:   137982
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: 50 (23.9 bits)

Align candidate WP_086509348.1 BZY95_RS07615 (succinyldiaminopimelate transaminase)
to HMM TIGR03538 (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/TIGR03538.hmm
# target sequence database:        /tmp/gapView.30430.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03538  [M=395]
Accession:   TIGR03538
Description: DapC_gpp: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-191  619.9   0.0     1e-190  619.6   0.0    1.1  1  lcl|NCBI__GCF_002151265.1:WP_086509348.1  BZY95_RS07615 succinyldiaminopim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509348.1  BZY95_RS07615 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  619.6   0.0    1e-190    1e-190       1     395 []       1     404 [.       1     404 [. 0.97

  Alignments for each domain:
  == domain 1  score: 619.6 bits;  conditional E-value: 1e-190
                                 TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpe 69 
                                               mnp+l++lkpyPfekla+l+++vtppa+l +i+l+iGeP+ha+ a  l +l ++  ++++yP+t+G+pe
  lcl|NCBI__GCF_002151265.1:WP_086509348.1   1 MNPDLDALKPYPFEKLATLKAGVTPPAQLAHIPLTIGEPQHAPFAGALATLHAHQLDFARYPATSGIPE 69 
                                               9******************************************************************** PP

                                 TIGR03538  70 lreaiaeWlerrfelpagvdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaallag 138
                                               lr aia+W++rrf+l   +dperqvlPvnGtrea+fafvqa +dr++ a v +PnPfyqiyeGa+llag
  lcl|NCBI__GCF_002151265.1:WP_086509348.1  70 LRGAIAAWARRRFRLDG-LDPERQVLPVNGTREAIFAFVQAALDRSRPARVAVPNPFYQIYEGATLLAG 137
                                               **************986.*************************************************** PP

                                 TIGR03538 139 aepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdec 207
                                               ++p++l+c ae+gf+pdfdavp+evW++vq+lf+csPgnPtGav +  e++kl++lad++dfiiasdec
  lcl|NCBI__GCF_002151265.1:WP_086509348.1 138 GQPHYLDCRAESGFRPDFDAVPAEVWREVQILFLCSPGNPTGAVTPRAEFQKLIALADEFDFIIASDEC 206
                                               ********************************************************************* PP

                                 TIGR03538 208 yselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGc 276
                                               yselylde+++P Gllea+a++Gr+d++r+lvfhslskrsn+PGlrsGfvaGdael++ f+ryrtyhGc
  lcl|NCBI__GCF_002151265.1:WP_086509348.1 207 YSELYLDEDAPPPGLLEACAAMGRHDYRRCLVFHSLSKRSNLPGLRSGFVAGDAELIAPFKRYRTYHGC 275
                                               ********************************************************************* PP

                                 TIGR03538 277 ampiavqlasiaaWedekhvrenralyrekfaavleilgavldlelPdasfylWlkvpdgddeafaral 345
                                               am+++ q+asi+aW+de+hvr+nr++yrekfaav+eil++vl++ +P+asfylW++vp gddeaf+r+l
  lcl|NCBI__GCF_002151265.1:WP_086509348.1 276 AMSLPLQHASITAWNDEAHVRANRDAYREKFAAVTEILAPVLEFPAPEASFYLWPAVPGGDDEAFTREL 344
                                               ********************************************************************* PP

                                 TIGR03538 346 yeeenvkvlpGrylsreae..........gvnPGegrvrlalvaeleecveaaerikkll 395
                                               +++e+v vlpG+y++r +           g nPG+gr+rlalvaele +veaa ri++++
  lcl|NCBI__GCF_002151265.1:WP_086509348.1 345 FAAEHVSVLPGSYMGRPTTgdgrgradgrGDNPGAGRIRLALVAELEPTVEAAGRIRRFI 404
                                               ***************97642222222222579*************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (408 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: 00:00:00.02
# Mc/sec: 7.81
//
[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