GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Phyllobacterium endophyticum PEPV15

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_106719128.1 CU100_RS23855 phosphoserine transaminase

Query= metacyc::MONOMER-15918
         (370 letters)



>NCBI__GCF_003010935.1:WP_106719128.1
          Length = 391

 Score =  484 bits (1246), Expect = e-141
 Identities = 236/379 (62%), Positives = 280/379 (73%), Gaps = 10/379 (2%)

Query: 2   KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61
           KP + P NP FSSGPCAK PG+S++ L D P GRSHR+K GK+KL +AI  TR++L +P 
Sbjct: 6   KPAQRPANPNFSSGPCAKRPGWSLDALSDAPLGRSHRAKVGKDKLKQAIDLTREILQVPA 65

Query: 62  DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121
           DY +GIVPASDTGA EM LWS+LG RGVD++ WESF  GW TD+ KQLKL DTR+ EA Y
Sbjct: 66  DYRIGIVPASDTGAVEMALWSLLGERGVDMVAWESFGSGWVTDVIKQLKLGDTRIIEAAY 125

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181
           G LPDL  VDF  DVVF WNGTTSGV+VP+ D+IP DR+G+T+CDATSA FA  + + KL
Sbjct: 126 GDLPDLSSVDFDRDVVFTWNGTTSGVRVPDGDFIPADRKGLTICDATSAAFAQRLDFDKL 185

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241
           DV+TFSWQKVLGGEGAHGMLILSPRAV+RL +Y PAWPLPKIFRLT GGKL + IF+G T
Sbjct: 186 DVVTFSWQKVLGGEGAHGMLILSPRAVERLLTYKPAWPLPKIFRLTSGGKLIEGIFSGET 245

Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSML  ED+L  L WA+S+GGL  L+ R + N AV +AF+ +  WI  LA     RS
Sbjct: 246 INTPSMLCVEDYLDALTWAKSIGGLDGLVGRADRNFAVLDAFIERTPWIANLARVPATRS 305

Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351
           +TSVC  +          +      K L+  LEKE VAYDIG+YRDAPSGLRIW GATVE
Sbjct: 306 NTSVCLTIIDPDITALGTEAQANFAKSLVAVLEKEGVAYDIGAYRDAPSGLRIWAGATVE 365

Query: 352 KEDLECLCEWIEWAYNLVK 370
             DLE L  W+EWA+   K
Sbjct: 366 AADLEALTLWLEWAFQSQK 384


Lambda     K      H
   0.319    0.136    0.430 

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: 470
Number of extensions: 14
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: 370
Length of database: 391
Length adjustment: 30
Effective length of query: 340
Effective length of database: 361
Effective search space:   122740
Effective search space used:   122740
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_106719128.1 CU100_RS23855 (phosphoserine transaminase)
to HMM TIGR01365 (phosphoserine aminotransferase (EC 2.6.1.52))

# 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/TIGR01365.hmm
# target sequence database:        /tmp/gapView.4152971.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01365  [M=374]
Accession:   TIGR01365
Description: serC_2: phosphoserine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-217  707.2   0.3   2.9e-217  707.0   0.3    1.0  1  NCBI__GCF_003010935.1:WP_106719128.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106719128.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  707.0   0.3  2.9e-217  2.9e-217       1     373 [.      10     382 ..      10     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 707.0 bits;  conditional E-value: 2.9e-217
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           rpanp+fssgpcakrpg+s+++l +a+lgrshr+k+gk+klk+ai+ tre+l+vpady+igiv+asdtgavem
  NCBI__GCF_003010935.1:WP_106719128.1  10 RPANPNFSSGPCAKRPGWSLDALSDAPLGRSHRAKVGKDKLKQAIDLTREILQVPADYRIGIVPASDTGAVEM 82 
                                           7************************************************************************ PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           alwsllg+rgvd++a+esfg+gwvtdv+kqlkl d r++ea yg+lpdl+ vdf++dvvftwngttsgvrvp+
  NCBI__GCF_003010935.1:WP_106719128.1  83 ALWSLLGERGVDMVAWESFGSGWVTDVIKQLKLGDTRIIEAAYGDLPDLSSVDFDRDVVFTWNGTTSGVRVPD 155
                                           ************************************************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           gdfipadr+glticdatsaafaq+ld++kldvvtfswqkvlggegahg+lilsprav+rl +y+pawplpkif
  NCBI__GCF_003010935.1:WP_106719128.1 156 GDFIPADRKGLTICDATSAAFAQRLDFDKLDVVTFSWQKVLGGEGAHGMLILSPRAVERLLTYKPAWPLPKIF 228
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           rlt+ggkl+++if getintpsml+ved+ldal wa+siggl+ lv rad n avl+af+++++w+  la  +
  NCBI__GCF_003010935.1:WP_106719128.1 229 RLTSGGKLIEGIFSGETINTPSMLCVEDYLDALTWAKSIGGLDGLVGRADRNFAVLDAFIERTPWIANLARVP 301
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                           ++rsntsvcl ++dpd++al  +aqa+fak lv +lekegvaydig+yrdap+glriw gatve+ dleal+ 
  NCBI__GCF_003010935.1:WP_106719128.1 302 ATRSNTSVCLTIIDPDITALGTEAQANFAKSLVAVLEKEGVAYDIGAYRDAPSGLRIWAGATVEAADLEALTL 374
                                           ************************************************************************* PP

                             TIGR01365 366 wldwafal 373
                                           wl+waf+ 
  NCBI__GCF_003010935.1:WP_106719128.1 375 WLEWAFQS 382
                                           ******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.32
//
[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