Alignments for a candidate for serC in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Dechloromonas agitata is5

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_027458973.1 K420_RS0116250 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::Q9SHP0
         (422 letters)



>NCBI__GCF_000519045.1:WP_027458973.1
          Length = 361

 Score =  387 bits (995), Expect = e-112
 Identities = 198/361 (54%), Positives = 259/361 (71%), Gaps = 4/361 (1%)

Query: 62  RVINFAAGPAALPENVLLKAQSDLYNWRGSGMSVMEMSHRGKEFLSIIQKAESDLRQLLE 121
           R+ NF+AGPAALPE VL +AQ +L +W GSG SVMEMSHRGKEF SII++AE+DLR+L+ 
Sbjct: 3   RIHNFSAGPAALPEEVLKQAQEELLDWHGSGCSVMEMSHRGKEFTSIIEQAEADLRELMG 62

Query: 122 IPSEYSVLFLQGGATTQFAALPLNLCKSDDSVDYIVTGSWGDKAFKEAKKYCNPKVIWSG 181
           IP +Y VLFLQGGAT QFA +P+NL  +  S DYIVTGSW  KAFKEA++  N +   + 
Sbjct: 63  IPEQYKVLFLQGGATQQFAQIPMNLL-AGRSADYIVTGSWSKKAFKEAQRIGNVRCAATT 121

Query: 182 KSEKYTKVPTFDGLEQSSDAKYLHICANETIHGVEFKDYPLVENPDGV-LIADMSSNFCS 240
           ++  +T++P  + ++    A YLH+C NETIHGVE     + +   GV L+ADMSS+  S
Sbjct: 122 EASNFTRLPVAEEIKLDPFAAYLHVCTNETIHGVEIPAERIADT--GVPLVADMSSHILS 179

Query: 241 KPVDVSKFGVIYAGAQKNVGPSGVTIVIIRKDLIGNARDITPVMLDYKIHDENSSLYNTP 300
           +PV V KFG+IYAGAQKN+GPSGVT+VII +DL+G A    P ++DY +  EN S+ NTP
Sbjct: 180 RPVPVEKFGLIYAGAQKNIGPSGVTLVIIHRDLLGMAPLTIPTVMDYAVMAENGSMLNTP 239

Query: 301 PCFGIYMCGLVFDDLLEQGGLKEVEKKNQRKAELLYNAIDESRGFFRCPVEKSVRSLMNV 360
           P +GIY+ GLVF  L  QGGL+ + + N  KA +LY  ID+S GF+R PV+   RS MNV
Sbjct: 240 PTYGIYIAGLVFQWLKRQGGLEGMARINAEKARILYACIDQSGGFYRNPVDADCRSAMNV 299

Query: 361 PFTLEKSELEAEFIKEAAKEKMVQLKGHRSVGGMRASIYNAMPLAGVEKLVAFMKDFQAR 420
           PF L   +L+A+F+ E+    +  LKGH+SVGGMRASIYNA+ L  V+ LVAFM +F  R
Sbjct: 300 PFVLANPDLDAKFLAESKAAGLASLKGHKSVGGMRASIYNAVSLESVQALVAFMNEFAKR 359

Query: 421 H 421
           +
Sbjct: 360 N 360


Lambda     K      H
   0.317    0.133    0.383 

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: 412
Number of extensions: 9
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: 422
Length of database: 361
Length adjustment: 31
Effective length of query: 391
Effective length of database: 330
Effective search space:   129030
Effective search space used:   129030
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_027458973.1 K420_RS0116250 (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.26153.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-161  523.0   0.0   1.8e-161  522.9   0.0    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027458973.1  K420_RS0116250 3-phosphoserine/p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027458973.1  K420_RS0116250 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.9   0.0  1.8e-161  1.8e-161       1     357 [.       4     359 ..       4     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 522.9 bits;  conditional E-value: 1.8e-161
                                 TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 
                                               i+nFsaGPaalpeevl++aq+elld++g+g+svme+sHR kef++++e+ae dlreL+ ip++y+vlfl
  lcl|NCBI__GCF_000519045.1:WP_027458973.1   4 IHNFSAGPAALPEEVLKQAQEELLDWHGSGCSVMEMSHRGKEFTSIIEQAEADLRELMGIPEQYKVLFL 72 
                                               58******************************************************************* PP

                                 TIGR01364  70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138
                                               qGGat+qfa++p+nll+ +  adyivtG+wskka+kea+++++ v+ +a++e ++++++p  ee++l++
  lcl|NCBI__GCF_000519045.1:WP_027458973.1  73 QGGATQQFAQIPMNLLAGR-SADYIVTGSWSKKAFKEAQRIGN-VRCAATTEASNFTRLPVAEEIKLDP 139
                                               ****************987.9********************99.************************* PP

                                 TIGR01364 139 daayvylcanetieGvefk.elpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvviv 206
                                                aay+++c+neti+Gve+  e    + +plvaD+ss+ilsr++ v+k+gliyaGaqKniGp+Gvt+vi+
  lcl|NCBI__GCF_000519045.1:WP_027458973.1 140 FAAYLHVCTNETIHGVEIPaERIADTGVPLVADMSSHILSRPVPVEKFGLIYAGAQKNIGPSGVTLVII 208
                                               ******************956677788****************************************** PP

                                 TIGR01364 207 rkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYea 275
                                               ++dll+ a  ++p+v+dY+++aen s++ntppt++iy++glv++wlk++GG++ +++ n eKa++lY +
  lcl|NCBI__GCF_000519045.1:WP_027458973.1 209 HRDLLGMAPLTIPTVMDYAVMAENGSMLNTPPTYGIYIAGLVFQWLKRQGGLEGMARINAEKARILYAC 277
                                               ********************************************************************* PP

                                 TIGR01364 276 idesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleev 344
                                               id+s gfy+n+v++++Rs mnv+F l++ +l+++Fl+e++++gl slkGh+svGG+RasiYna++le+v
  lcl|NCBI__GCF_000519045.1:WP_027458973.1 278 IDQSGGFYRNPVDADCRSAMNVPFVLANPDLDAKFLAESKAAGLASLKGHKSVGGMRASIYNAVSLESV 346
                                               ********************************************************************* PP

                                 TIGR01364 345 qaLvdfmkeFekk 357
                                               qaLv+fm+eF+k+
  lcl|NCBI__GCF_000519045.1:WP_027458973.1 347 QALVAFMNEFAKR 359
                                               **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (361 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.21
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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 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 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