GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Salinicoccus carnicancri Crm

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_017549759.1 C792_RS0112315 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

Query= BRENDA::O67216
         (294 letters)



>NCBI__GCF_000330705.1:WP_017549759.1
          Length = 302

 Score =  251 bits (640), Expect = 2e-71
 Identities = 131/287 (45%), Positives = 183/287 (63%), Gaps = 1/287 (0%)

Query: 3   QGSIVALITPFKE-GEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEF 61
           +GSI  +ITPFKE G++D++    LIE+ +DNGT  I V GT+GE  +LT +E  +++E 
Sbjct: 13  RGSICPVITPFKENGDIDFDGQAGLIEYQLDNGTHCISVTGTSGEPSSLTTKERVQIMEH 72

Query: 62  AVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121
           A+K  AGR+    GTG     E ++LT  A+E+GAD A+V+VPYYNKP Q  LY+HFKTV
Sbjct: 73  AMKTIAGRVPFAPGTGSVNHDETMYLTKKAEEMGADAAMVIVPYYNKPNQDALYDHFKTV 132

Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181
           A  V IPIIIYNIP RT + ++  TM +L+ +C NIV  KES  + + ++ ++   G  F
Sbjct: 133 ADAVAIPIIIYNIPGRTALNMTAGTMARLSRDCPNIVGVKESNKDFEHVNRVMLNCGRDF 192

Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241
            + SG + L  PM+A+G  G IS   NV PR+V E+  A   GD  RA ++HY L +L  
Sbjct: 193 LLYSGIELLCYPMLAIGGAGSISATANVEPRKVAEMHDAWERGDRDRALDLHYELMNLND 252

Query: 242 VLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKY 288
           VLF +TNP PVK A  M+G  E   R P+   S + + ++RE L+ Y
Sbjct: 253 VLFKDTNPAPVKAALGMMGKIEPVLRKPMGMPSSKLQEEIRETLRTY 299


Lambda     K      H
   0.318    0.136    0.390 

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: 243
Number of extensions: 9
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: 294
Length of database: 302
Length adjustment: 26
Effective length of query: 268
Effective length of database: 276
Effective search space:    73968
Effective search space used:    73968
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: 48 (23.1 bits)

Align candidate WP_017549759.1 C792_RS0112315 (2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.3868302.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.2e-89  286.0   0.0    1.3e-89  285.8   0.0    1.0  1  NCBI__GCF_000330705.1:WP_017549759.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017549759.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.8   0.0   1.3e-89   1.3e-89       2     285 ..      15     298 ..      14     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 285.8 bits;  conditional E-value: 1.3e-89
                             TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 
                                           ++  +iTPfke+g++df+  + lie+q+++g+  i v Gt GE  +L+++E+++++e a+++ ++rvp   Gt
  NCBI__GCF_000330705.1:WP_017549759.1  15 SICPVITPFKENGDIDFDGQAGLIEYQLDNGTHCISVTGTSGEPSSLTTKERVQIMEHAMKTIAGRVPFAPGT 87 
                                           67789******************************************************************** PP

                             TIGR00674  75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147
                                           gs + +e++ ltk+ae++g+d+++v++PyYnkP+q  ly hfk++a++v +Pii+Yn+P+Rt+ +++  t++r
  NCBI__GCF_000330705.1:WP_017549759.1  88 GSVNHDETMYLTKKAEEMGADAAMVIVPYYNKPNQDALYDHFKTVADAVAIPIIIYNIPGRTALNMTAGTMAR 160
                                           ************************************************************************* PP

                             TIGR00674 148 Laeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaal 219
                                           L+++++ iv++Ke+++d e+v++++   + df ++sG + l  ++la+G++G iS ++nv p++++em  a+ 
  NCBI__GCF_000330705.1:WP_017549759.1 161 LSRDCPnIVGVKESNKDFEHVNRVMLNCGRDFLLYSGIELLCYPMLAIGGAGSISATANVEPRKVAEMHDAWE 233
                                           ****999****************************************************************** PP

                             TIGR00674 220 egdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285
                                           +gd ++a+ +h++l++l ++lf +tNP pvK+al ++g ie   lR P+   s++ +e+++e+l++
  NCBI__GCF_000330705.1:WP_017549759.1 234 RGDRDRALDLHYELMNLNDVLFKDTNPAPVKAALGMMGKIEP-VLRKPMGMPSSKLQEEIRETLRT 298
                                           *****************************************9.*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (302 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: 17.76
//
[ok]

This GapMind analysis is from Jul 26 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:

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