GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Xanthobacter autotrophicus Py2

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_012113223.1 XAUT_RS06035 phosphoserine transaminase

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



>NCBI__GCF_000017645.1:WP_012113223.1
          Length = 391

 Score =  482 bits (1241), Expect = e-141
 Identities = 235/378 (62%), Positives = 275/378 (72%), Gaps = 10/378 (2%)

Query: 3   PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62
           PT  P+NP FSSGPCAK PG+++E L D P GRSHR+K GK KL EAI  TRD+L +P D
Sbjct: 7   PTTRPENPNFSSGPCAKRPGWTLEALSDAPLGRSHRAKVGKAKLKEAIDLTRDVLEVPAD 66

Query: 63  YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122
           Y +GIVPASDTGA EM LWSMLG R VD+L WESF +GW TD+ KQLKL D R   A YG
Sbjct: 67  YKIGIVPASDTGAVEMVLWSMLGARPVDMLAWESFGEGWVTDVVKQLKLTDARALTAPYG 126

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182
            LPDL +VDF +DVVF WNGTTSGV VP+A+WIP DR G+T+CDATSA FA  + + KLD
Sbjct: 127 ALPDLTQVDFSHDVVFTWNGTTSGVMVPDAEWIPADRTGLTICDATSAAFAQKLDFAKLD 186

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242
           V+TFSWQKVLGGEGAHG+LILSPRAV+RLE+Y PAWPLPKIFR+TKGGKL + IF G TI
Sbjct: 187 VVTFSWQKVLGGEGAHGILILSPRAVERLETYKPAWPLPKIFRMTKGGKLIEGIFEGETI 246

Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSML  ED+L  LKWA++VGGL  L  R+N N      +V    W+ FLA     RS+
Sbjct: 247 NTPSMLCVEDYLDALKWAKNVGGLSALQERSNRNFEAIAQWVHNTPWVDFLATDPVTRSN 306

Query: 303 TSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352
           TSVC KV          D      K +   LEK  +AYDIG+YRDAP GLRIWCGATVE+
Sbjct: 307 TSVCLKVVDADVTSLPADAQAAFAKAIASGLEKGGIAYDIGAYRDAPPGLRIWCGATVER 366

Query: 353 EDLECLCEWIEWAYNLVK 370
            D+E L  W++WA+   K
Sbjct: 367 ADVEALTHWLDWAFTEAK 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: 511
Number of extensions: 17
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_012113223.1 XAUT_RS06035 (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.2495791.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-214  696.9   1.1   3.8e-214  696.7   1.1    1.0  1  NCBI__GCF_000017645.1:WP_012113223.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_012113223.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.7   1.1  3.8e-214  3.8e-214       1     372 [.      10     381 ..      10     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 696.7 bits;  conditional E-value: 3.8e-214
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           rp+np+fssgpcakrpg+++e+l +a+lgrshr+k+gk+klkeai+ tr+vlevpady+igiv+asdtgavem
  NCBI__GCF_000017645.1:WP_012113223.1  10 RPENPNFSSGPCAKRPGWTLEALSDAPLGRSHRAKVGKAKLKEAIDLTRDVLEVPADYKIGIVPASDTGAVEM 82 
                                           79*********************************************************************** PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           +lws+lgar+vd+la+esfg+gwvtdv+kqlkl d r l a+yg lpdl++vdf++dvvftwngttsgv vp+
  NCBI__GCF_000017645.1:WP_012113223.1  83 VLWSMLGARPVDMLAWESFGEGWVTDVVKQLKLTDARALTAPYGALPDLTQVDFSHDVVFTWNGTTSGVMVPD 155
                                           ************************************************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           +++ipadr glticdatsaafaq+ld+ kldvvtfswqkvlggegahg+lilsprav+rle+y+pawplpkif
  NCBI__GCF_000017645.1:WP_012113223.1 156 AEWIPADRTGLTICDATSAAFAQKLDFAKLDVVTFSWQKVLGGEGAHGILILSPRAVERLETYKPAWPLPKIF 228
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           r+tkggkl+++ifegetintpsml+ved+ldalkwa+ +ggl+al++r++ n + ++++v +++wvdfla+ +
  NCBI__GCF_000017645.1:WP_012113223.1 229 RMTKGGKLIEGIFEGETINTPSMLCVEDYLDALKWAKNVGGLSALQERSNRNFEAIAQWVHNTPWVDFLATDP 301
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                            +rsntsvclkvvd dv+ l++daqa fak ++s lek g+aydig+yrdap+glriwcgatve+ d+eal++
  NCBI__GCF_000017645.1:WP_012113223.1 302 VTRSNTSVCLKVVDADVTSLPADAQAAFAKAIASGLEKGGIAYDIGAYRDAPPGLRIWCGATVERADVEALTH 374
                                           ************************************************************************* PP

                             TIGR01365 366 wldwafa 372
                                           wldwaf+
  NCBI__GCF_000017645.1:WP_012113223.1 375 WLDWAFT 381
                                           *****97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 23.04
//
[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