Aligments for a candidate for serC in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for serC in Caulobacter crescentus NA1000

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate CCNA_03323 CCNA_03323 phosphoserine aminotransferase

Query= BRENDA::P52878
         (370 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03323 CCNA_03323 phosphoserine
           aminotransferase
          Length = 396

 Score =  459 bits (1180), Expect = e-134
 Identities = 229/383 (59%), Positives = 275/383 (71%), Gaps = 15/383 (3%)

Query: 2   KPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPD 61
           KP   P  P FSSGPCAK PG++ E L++   GRSHRS LGK +L  AI +TR++L +P 
Sbjct: 7   KPAIRPARPEFSSGPCAKRPGWTPENLRNAVLGRSHRSKLGKARLKAAIDQTREVLEVPA 66

Query: 62  DYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEY 121
           D+L+GIV  SDTGA EM +WSMLG R V +L +ESF K W TD+TKQLKL DV V  A Y
Sbjct: 67  DFLIGIVAGSDTGAVEMAMWSMLGARPVQLLAFESFGKDWVTDVTKQLKLPDVEVLSAPY 126

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKL 181
           G+LPD  KVD   D+VF WNGTTSGV+VPN D+I  +REG+T+CDATSA FA D+ + KL
Sbjct: 127 GQLPDTSKVDPAKDLVFTWNGTTSGVRVPNADFISADREGITICDATSAAFAQDLDWTKL 186

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTK-----GGKLNKKI 236
           DV+TFSWQK LGGEGAHG+LILSPRAV RLESYTPAWP+PK+FR+TK     G K++  I
Sbjct: 187 DVVTFSWQKALGGEGAHGVLILSPRAVARLESYTPAWPMPKLFRMTKANKDGGNKVSLDI 246

Query: 237 FEGSTINTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAET 296
           FEG+TINTPSML  ED L  LKWA S+GGL+ +  R + NL V   +VAK  W+ FLA T
Sbjct: 247 FEGATINTPSMLCVEDALDALKWASSIGGLQAMQARADQNLKVLADWVAKTPWVDFLAAT 306

Query: 297 KEIRSSTSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWC 346
            EIRS+TSVC KV          D   +  K+L   LEKE  A DIG YRDAP+GLRIWC
Sbjct: 307 PEIRSNTSVCLKVVDPAICALPEDAQADFAKKLASLLEKEGAALDIGGYRDAPAGLRIWC 366

Query: 347 GATVEKEDLQCLCEWIEWAYNLV 369
           GATVE  DL+ L  W++WA+  V
Sbjct: 367 GATVEASDLEALTPWLDWAFATV 389


Lambda     K      H
   0.318    0.136    0.429 

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: 485
Number of extensions: 17
Number of successful extensions: 3
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: 396
Length adjustment: 30
Effective length of query: 340
Effective length of database: 366
Effective search space:   124440
Effective search space used:   124440
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_03323 CCNA_03323 (phosphoserine aminotransferase)
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.1454.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-234  763.8   1.5   1.7e-234  763.6   1.5    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03323  CCNA_03323 phosphoserine aminotr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03323  CCNA_03323 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  763.6   1.5  1.7e-234  1.7e-234       1     374 []      11     389 ..      11     389 .. 1.00

  Alignments for each domain:
  == domain 1  score: 763.6 bits;  conditional E-value: 1.7e-234
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           rpa+pefssgpcakrpg+++e+l+na+lgrshrsklgk++lk+ai++trevlevpad+ligiva+sdtgavem
  lcl|FitnessBrowser__Caulo:CCNA_03323  11 RPARPEFSSGPCAKRPGWTPENLRNAVLGRSHRSKLGKARLKAAIDQTREVLEVPADFLIGIVAGSDTGAVEM 83 
                                           7************************************************************************ PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           a+ws+lgar+v+llafesfgk+wvtdvtkqlkl+dv+vl+a+yg+lpd++kvd++kd+vftwngttsgvrvpn
  lcl|FitnessBrowser__Caulo:CCNA_03323  84 AMWSMLGARPVQLLAFESFGKDWVTDVTKQLKLPDVEVLSAPYGQLPDTSKVDPAKDLVFTWNGTTSGVRVPN 156
                                           ************************************************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           +dfi+adreg+ticdatsaafaqdld++kldvvtfswqk+lggegahgvlilspravarlesytpawp+pk+f
  lcl|FitnessBrowser__Caulo:CCNA_03323 157 ADFISADREGITICDATSAAFAQDLDWTKLDVVTFSWQKALGGEGAHGVLILSPRAVARLESYTPAWPMPKLF 229
                                           ************************************************************************* PP

                             TIGR01365 220 rltk.....ggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdf 287
                                           r+tk     g+k+s difeg+tintpsml+vedaldalkwa+siggl+a++arad+nl+vl+++vak++wvdf
  lcl|FitnessBrowser__Caulo:CCNA_03323 230 RMTKankdgGNKVSLDIFEGATINTPSMLCVEDALDALKWASSIGGLQAMQARADQNLKVLADWVAKTPWVDF 302
                                           ********99*************************************************************** PP

                             TIGR01365 288 laatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdl 360
                                           laat+eirsntsvclkvvdp+++al+edaqadfak+l+s+lekeg+a+dig+yrdapaglriwcgatve+sdl
  lcl|FitnessBrowser__Caulo:CCNA_03323 303 LAATPEIRSNTSVCLKVVDPAICALPEDAQADFAKKLASLLEKEGAALDIGGYRDAPAGLRIWCGATVEASDL 375
                                           ************************************************************************* PP

                             TIGR01365 361 eallewldwafalv 374
                                           eal++wldwafa+v
  lcl|FitnessBrowser__Caulo:CCNA_03323 376 EALTPWLDWAFATV 389
                                           ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (396 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: 00:00:00.02
# Mc/sec: 7.09
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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