Aligments for a candidate for dapC in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapC in Sphingomonas koreensis DSMZ 15582

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Ga0059261_2265 Ga0059261_2265 phosphoserine aminotransferase apoenzyme (EC 2.6.1.52)

Query= BRENDA::P52878
         (370 letters)



>FitnessBrowser__Korea:Ga0059261_2265
          Length = 378

 Score =  456 bits (1174), Expect = e-133
 Identities = 219/369 (59%), Positives = 269/369 (72%), Gaps = 2/369 (0%)

Query: 3   PTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDD 62
           P   P  P FSSGPCAK PG+S ++L     GRSHRS LGK +L  AI   R+ML LPD 
Sbjct: 8   PATKPARPYFSSGPCAKPPGWSADKLHTEVLGRSHRSKLGKTRLQYAIDLMREMLKLPDT 67

Query: 63  YLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYG 122
           + +GIVP SDTGAFEM +W+MLG RGV  L WESF +GW TD  KQLKL D  V  A+YG
Sbjct: 68  HRIGIVPGSDTGAFEMAMWTMLGARGVTTLAWESFGEGWVTDAVKQLKL-DPTVIRADYG 126

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLD 182
           +LPDL +VDF +DV+F WNGTTSGV+VPNGDWIP++REGLT  D+TSA+FA D+P+ K+D
Sbjct: 127 QLPDLSQVDFADDVLFTWNGTTSGVRVPNGDWIPDDREGLTFADSTSAVFAYDLPWDKID 186

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGSTI 242
           V TFSWQKVLGGEG HG+LIL PRAV+RLE YTPAWPLPK+FRL   GKL + +F+G TI
Sbjct: 187 VATFSWQKVLGGEGGHGVLILGPRAVERLEQYTPAWPLPKVFRLMAKGKLAEGVFKGETI 246

Query: 243 NTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSMLA ED +  L+WA+ +GGL  LI R++ N A  +  VA+ +W+  LA  +  RS 
Sbjct: 247 NTPSMLAVEDAIFALEWAKGLGGLDGLIARSDANAAALDKIVAERDWLGHLAADEATRSK 306

Query: 303 TSVCFKVDLSDEK-LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLQCLCEW 361
           TSVC  V+ +DE  +K     LEK   AYD+  YRDAP+GLRIWCGATV+  D++ L  W
Sbjct: 307 TSVCLTVEGADEAFIKTFASLLEKADAAYDVAGYRDAPAGLRIWCGATVDTADIEALGPW 366

Query: 362 IEWAYNLVK 370
           ++WAY   K
Sbjct: 367 LDWAYASAK 375


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: 489
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: 378
Length adjustment: 30
Effective length of query: 340
Effective length of database: 348
Effective search space:   118320
Effective search space used:   118320
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 Ga0059261_2265 Ga0059261_2265 (phosphoserine aminotransferase apoenzyme (EC 2.6.1.52))
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.15017.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     9e-183  593.5   0.5     1e-182  593.2   0.5    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2265  Ga0059261_2265 phosphoserine ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2265  Ga0059261_2265 phosphoserine aminotransferase apoenzyme (EC 2.6.1.52)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  593.2   0.5    1e-182    1e-182       1     373 [.      11     373 ..      11     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 593.2 bits;  conditional E-value: 1e-182
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               +pa+p fssgpcak pg+s ++l+  +lgrshrsklgk++l+ ai+  re+l++p+ ++igiv++sdtg
  lcl|FitnessBrowser__Korea:Ga0059261_2265  11 KPARPYFSSGPCAKPPGWSADKLHTEVLGRSHRSKLGKTRLQYAIDLMREMLKLPDTHRIGIVPGSDTG 79 
                                               69******************************************************************* PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138
                                               a+ema+w++lgargv  la+esfg+gwvtd +kqlkl d  v+ a+yg+lpdl++vdf+ dv+ftwngt
  lcl|FitnessBrowser__Korea:Ga0059261_2265  80 AFEMAMWTMLGARGVTTLAWESFGEGWVTDAVKQLKL-DPTVIRADYGQLPDLSQVDFADDVLFTWNGT 147
                                               ************************************9.6789*************************** PP

                                 TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207
                                               tsgvrvpngd+ip+dreglt+ d+tsa+fa dl+++k+dv tfswqkvlggeg hgvlil prav+rle
  lcl|FitnessBrowser__Korea:Ga0059261_2265 148 TSGVRVPNGDWIPDDREGLTFADSTSAVFAYDLPWDKIDVATFSWQKVLGGEGGHGVLILGPRAVERLE 216
                                               ********************************************************************* PP

                                 TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276
                                                ytpawplpk+frl   gkl++++f+getintpsmlaveda+ al+wa+ +ggl+ l+ar+d+n+a l+
  lcl|FitnessBrowser__Korea:Ga0059261_2265 217 QYTPAWPLPKVFRLMAKGKLAEGVFKGETINTPSMLAVEDAIFALEWAKGLGGLDGLIARSDANAAALD 285
                                               ********************************************************************* PP

                                 TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345
                                               + va  +w+++laa +++rs+tsvcl v         e a+  f+k ++s+lek ++ayd+ +yrdapa
  lcl|FitnessBrowser__Korea:Ga0059261_2265 286 KIVAERDWLGHLAADEATRSKTSVCLTV---------EGADEAFIKTFASLLEKADAAYDVAGYRDAPA 345
                                               ***************************9.........444456************************** PP

                                 TIGR01365 346 glriwcgatveksdleallewldwafal 373
                                               glriwcgatv++ d+eal +wldwa+a 
  lcl|FitnessBrowser__Korea:Ga0059261_2265 346 GLRIWCGATVDTADIEALGPWLDWAYAS 373
                                               **************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (378 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.93
//
[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