GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Kyrpidia tusciae DSM 2912

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_013075035.1 BTUS_RS05070 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::Q59196
         (362 letters)



>NCBI__GCF_000092905.1:WP_013075035.1
          Length = 364

 Score =  457 bits (1177), Expect = e-133
 Identities = 223/357 (62%), Positives = 278/357 (77%)

Query: 3   KRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALL 62
           KRA NFNAGPAALPLEVLE+A+ EFVD+  TGMS+MEMSHR   YEA+HNE  A +  LL
Sbjct: 5   KRALNFNAGPAALPLEVLEQAREEFVDFGGTGMSVMEMSHRSKTYEAIHNETAALVRELL 64

Query: 63  GNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAAS 122
           G P GY VLF+QGGAS QFAM+PMNFL +G+ A YV+TGSW+ KALKEA+ +G+T VAAS
Sbjct: 65  GVPEGYDVLFLQGGASLQFAMVPMNFLPKGKAAGYVLTGSWSEKALKEAQRLGETFVAAS 124

Query: 123 SEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRP 182
           ++  +Y  +P  +EI    ++AYLH+TSN TI G Q+  FPDTGSVPL+ DMSSDILSR 
Sbjct: 125 TKDGHYRRIPGAEEISFGRDSAYLHVTSNNTIFGTQWTRFPDTGSVPLVADMSSDILSRK 184

Query: 183 FDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPS 242
            D+ QF L+YAGAQKNLGPSGVT+V+VR+D+V  +P+ LPTML+Y  + KNNSLYNTPP+
Sbjct: 185 IDVRQFALIYAGAQKNLGPSGVTLVVVRQDMVERAPEDLPTMLQYRIHAKNNSLYNTPPT 244

Query: 243 FGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITF 302
           FGIYM+  VLKW++ +GG+E V++ NR+KA LIY  ID +  FY G  +  SRS MN+TF
Sbjct: 245 FGIYMMGLVLKWVKGQGGVEAVERRNREKAGLIYKVIDDNPDFYLGHAEPTSRSLMNVTF 304

Query: 303 RLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKR 359
           RL + ELEKEF+  ++ EGFVGL GHRSVGG RAS+YNAVP E C AL  +M  F++
Sbjct: 305 RLPTPELEKEFLDGAKAEGFVGLNGHRSVGGCRASLYNAVPVEHCAALRDYMVEFRK 361


Lambda     K      H
   0.316    0.132    0.378 

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: 437
Number of extensions: 9
Number of successful extensions: 1
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: 362
Length of database: 364
Length adjustment: 29
Effective length of query: 333
Effective length of database: 335
Effective search space:   111555
Effective search space used:   111555
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_013075035.1 BTUS_RS05070 (3-phosphoserine/phosphohydroxythreonine transaminase)
to HMM TIGR01364 (serC: phosphoserine transaminase (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/TIGR01364.hmm
# target sequence database:        /tmp/gapView.3699011.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01364  [M=358]
Accession:   TIGR01364
Description: serC_1: phosphoserine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-158  513.3   0.0   1.7e-158  513.1   0.0    1.0  1  NCBI__GCF_000092905.1:WP_013075035.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092905.1:WP_013075035.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.1   0.0  1.7e-158  1.7e-158       2     358 .]       8     363 ..       7     363 .. 0.99

  Alignments for each domain:
  == domain 1  score: 513.1 bits;  conditional E-value: 1.7e-158
                             TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGat 74 
                                            nF+aGPaalp evle+a++e++df g+g+svme+sHRsk++e++++e+   +reLl +p+ y+vlflqGGa+
  NCBI__GCF_000092905.1:WP_013075035.1   8 LNFNAGPAALPLEVLEQAREEFVDFGGTGMSVMEMSHRSKTYEAIHNETAALVRELLGVPEGYDVLFLQGGAS 80 
                                           69*********************************************************************** PP

                             TIGR01364  75 tqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylca 147
                                            qfa+vp+n+l ++k a y+ tG+ws+kalkea++l++ + v+as+++++y +ip  ee+++  d+ay+++++
  NCBI__GCF_000092905.1:WP_013075035.1  81 LQFAMVPMNFLPKGKAAGYVLTGSWSEKALKEAQRLGE-TFVAASTKDGHYRRIPGAEEISFGRDSAYLHVTS 152
                                           ************************************98.8999999*************************** PP

                             TIGR01364 148 netieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelps 220
                                           n+ti G+++++ p++ ++plvaD+ssdilsrkidv +++liyaGaqKn+Gp+Gvt+v+vr+d++era ++lp+
  NCBI__GCF_000092905.1:WP_013075035.1 153 NNTIFGTQWTRFPDTGSVPLVADMSSDILSRKIDVRQFALIYAGAQKNLGPSGVTLVVVRQDMVERAPEDLPT 225
                                           ************************************************************************* PP

                             TIGR01364 221 vldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRs 293
                                           +l+Y+i+a+n+slyntpptf+iy++glvlkw+k +GGv+++e++n+eKa l+Y++id++ +fy +++e+++Rs
  NCBI__GCF_000092905.1:WP_013075035.1 226 MLQYRIHAKNNSLYNTPPTFGIYMMGLVLKWVKGQGGVEAVERRNREKAGLIYKVIDDNPDFYLGHAEPTSRS 298
                                           ************************************************************************* PP

                             TIGR01364 294 lmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                           lmnv+F+l+  elekeFl+ a+++g+v+l+GhrsvGG+Ras+Yna+p+e++ aL d+m eF+kkh
  NCBI__GCF_000092905.1:WP_013075035.1 299 LMNVTFRLPTPELEKEFLDGAKAEGFVGLNGHRSVGGCRASLYNAVPVEHCAALRDYMVEFRKKH 363
                                           **************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (364 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: 15.37
//
[ok]

This GapMind analysis is from Jul 25 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