Alignments for a candidate for serC in Sphingomonas indica Dd16

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Sphingomonas indica Dd16

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_085218337.1 B9N75_RS08135 phosphoserine transaminase

Query= SwissProt::P52878
         (370 letters)



>NCBI__GCF_900177405.1:WP_085218337.1
          Length = 398

 Score =  442 bits (1136), Expect = e-128
 Identities = 220/373 (58%), Positives = 264/373 (70%), Gaps = 9/373 (2%)

Query: 2   KPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPD 61
           KP+  P  P FSSGPCAK PG+  E L     GRSHRS +GK +L  AI  TR +L +PD
Sbjct: 21  KPSDKPRRPHFSSGPCAKPPGWGPEHLATGSLGRSHRSKIGKARLHHAIDLTRKLLRVPD 80

Query: 62  DYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEY 121
            + +GIVP SDTGA EM +W+MLG R V +L WESF +GW TD  KQL+L D +V  A Y
Sbjct: 81  THRIGIVPGSDTGAVEMAMWTMLGARPVTMLAWESFGEGWVTDAVKQLRL-DAKVMTAPY 139

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKL 181
           G LPDL  VD  +DVVF WNGTTSGV+VP+G WI + REGLT+CDATSA FAM++ + KL
Sbjct: 140 GALPDLGAVDPGHDVVFTWNGTTSGVRVPDGGWIGDAREGLTICDATSAAFAMELQWDKL 199

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGST 241
           DV TFSWQKV+GGEGAHG+LIL PRAV+RLE+YTPAWPLPK+FRLTKGGKLN+ IF+G T
Sbjct: 200 DVTTFSWQKVMGGEGAHGILILGPRAVERLETYTPAWPLPKLFRLTKGGKLNEGIFQGET 259

Query: 242 INTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSMLA ED++  L+WA+ +GGL  LI R   N    +A+V +  WI  LA     RS
Sbjct: 260 INTPSMLAVEDYIFALEWAQGLGGLPALIGRCEANARALDAWVERTPWIAHLAADPATRS 319

Query: 302 STSVCF----KVDLSDEKLKELIKT----LEKEKVAYDIGSYRDAPSGLRIWCGATVEKE 353
           +TSVC        L D     L+K     LE E  A+DI SYRDAP GLRIWCGATVE  
Sbjct: 320 TTSVCLAFAAAAGLDDAAAAALVKAMASLLENEGAAFDIASYRDAPPGLRIWCGATVETA 379

Query: 354 DLQCLCEWIEWAY 366
           D++ L  W++WAY
Sbjct: 380 DIEALGPWLDWAY 392


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: 506
Number of extensions: 19
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: 398
Length adjustment: 30
Effective length of query: 340
Effective length of database: 368
Effective search space:   125120
Effective search space used:   125120
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 WP_085218337.1 B9N75_RS08135 (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.3053063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-190  618.6   0.1   2.3e-190  618.4   0.1    1.0  1  NCBI__GCF_900177405.1:WP_085218337.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085218337.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.4   0.1  2.3e-190  2.3e-190       1     373 [.      25     394 ..      25     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 618.4 bits;  conditional E-value: 2.3e-190
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           +p +p+fssgpcak pg+ +e+l   +lgrshrsk+gk++l++ai+ tr++l+vp+ ++igiv++sdtgavem
  NCBI__GCF_900177405.1:WP_085218337.1  25 KPRRPHFSSGPCAKPPGWGPEHLATGSLGRSHRSKIGKARLHHAIDLTRKLLRVPDTHRIGIVPGSDTGAVEM 97 
                                           599********************************************************************** PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           a+w++lgar+v +la+esfg+gwvtd +kql+l d +v+ a+yg lpdl  vd+ +dvvftwngttsgvrvp+
  NCBI__GCF_900177405.1:WP_085218337.1  98 AMWTMLGARPVTMLAWESFGEGWVTDAVKQLRL-DAKVMTAPYGALPDLGAVDPGHDVVFTWNGTTSGVRVPD 169
                                           ********************************9.89************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           g +i + reglticdatsaafa++l+++kldv tfswqkv+ggegahg+lil prav+rle+ytpawplpk+f
  NCBI__GCF_900177405.1:WP_085218337.1 170 GGWIGDAREGLTICDATSAAFAMELQWDKLDVTTFSWQKVMGGEGAHGILILGPRAVERLETYTPAWPLPKLF 242
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           rltkggkl+++if+getintpsmlaved++ al+wa+ +ggl al+ r+++n++ l+a+v++++w+ +laa +
  NCBI__GCF_900177405.1:WP_085218337.1 243 RLTKGGKLNEGIFQGETINTPSMLAVEDYIFALEWAQGLGGLPALIGRCEANARALDAWVERTPWIAHLAADP 315
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                           ++rs+tsvcl +   + a ld+ a a ++k ++s+le+eg+a+di syrdap+glriwcgatve+ d+eal +
  NCBI__GCF_900177405.1:WP_085218337.1 316 ATRSTTSVCLAF--AAAAGLDDAAAAALVKAMASLLENEGAAFDIASYRDAPPGLRIWCGATVETADIEALGP 386
                                           ************..7788999999************************************************* PP

                             TIGR01365 366 wldwafal 373
                                           wldwa+a+
  NCBI__GCF_900177405.1:WP_085218337.1 387 WLDWAYAT 394
                                           ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (398 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: 29.35
//
[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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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