Alignments for a candidate for dapC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pedobacter sp. GW460-11-11-14-LB5

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate CA265_RS03895 CA265_RS03895 phosphoserine transaminase

Query= SwissProt::Q9RME2
         (361 letters)



>FitnessBrowser__Pedo557:CA265_RS03895
          Length = 365

 Score =  320 bits (820), Expect = 4e-92
 Identities = 165/353 (46%), Positives = 235/353 (66%), Gaps = 4/353 (1%)

Query: 7   NFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPN 66
           NF AGP  LP   +E+A + ++N+    +S++E+SHRS  +E+V  + Q L+RELL +PN
Sbjct: 6   NFGAGPCILPSSVMEQAAQAVINWGGMGLSILEVSHRSPEFEDVVLKTQLLVRELLSVPN 65

Query: 67  DYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKAN 126
            Y +LFLQGGAS QF M+ MN L+ G    Y+ TG +++KA+KEAKL GE  + AS+K  
Sbjct: 66  HYSVLFLQGGASTQFAMVAMNFLSAGKKAAYLDTGYFAQKAIKEAKLFGEVELVASSKDK 125

Query: 127 SYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVN 186
            Y  IPD  +F +++  AY+H TSNNTI GT+  +F   N  P++ DMSSDI SR + V+
Sbjct: 126 DYAYIPD--QFNVDQESAYIHYTSNNTIEGTEIFDFSP-NGVPVVCDMSSDIFSRKINVS 182

Query: 187 QFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIY 246
            F +IYAGAQKN+GP+G+T+VI K + LN   +++P+M+ Y     + S+YNTPP FSIY
Sbjct: 183 DFDLIYAGAQKNMGPAGMTLVIAKNEFLNQAKKEIPSMMDYRIFRDNMSMYNTPPVFSIY 242

Query: 247 MLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRN 306
           +    L W+KD GG   I ++N EKAK++Y  ID +  FY G A+   RS MNVTF   N
Sbjct: 243 VAMLNLLWLKDQGGVSGIEQRNIEKAKLLYAEIDRNPLFY-GTADVAHRSRMNVTFLAVN 301

Query: 307 EELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKE 359
           +++   FL  A +QG VG+ G+R+VGG RAS+YNA+P+ +   L   M  F++
Sbjct: 302 KDVEGGFLKFAADQGIVGIKGYRTVGGFRASLYNALPLSSVEVLVNAMASFEK 354


Lambda     K      H
   0.316    0.132    0.372 

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: 350
Number of extensions: 10
Number of successful extensions: 4
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: 361
Length of database: 365
Length adjustment: 29
Effective length of query: 332
Effective length of database: 336
Effective search space:   111552
Effective search space used:   111552
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 CA265_RS03895 CA265_RS03895 (phosphoserine 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.8771.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.2e-141  456.3   0.4   3.6e-141  456.1   0.4    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS03895  CA265_RS03895 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS03895  CA265_RS03895 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.1   0.4  3.6e-141  3.6e-141       2     357 ..       5     355 ..       4     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.1 bits;  conditional E-value: 3.6e-141
                                  TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 
                                                +nF+aGP++lp++v+e+a++ ++++ g+gls++e+sHRs efe+vv +++  +reLl++p++y+vlfl
  lcl|FitnessBrowser__Pedo557:CA265_RS03895   5 HNFGAGPCILPSSVMEQAAQAVINWGGMGLSILEVSHRSPEFEDVVLKTQLLVRELLSVPNHYSVLFL 72 
                                                8******************************************************************* PP

                                  TIGR01364  70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelk 137
                                                qGGa+tqfa+v++n+l+++k+a+y+ tG++++ka+keak +++ v+ vas+++k+y  ip  ++++++
  lcl|FitnessBrowser__Pedo557:CA265_RS03895  73 QGGASTQFAMVAMNFLSAGKKAAYLDTGYFAQKAIKEAKLFGE-VELVASSKDKDYAYIP--DQFNVD 137
                                                *****************************************88.****************..789999 PP

                                  TIGR01364 138 edaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvi 205
                                                +++ay+++++n+tieG+e+ +    + +p+v+D+ssdi+srki+vs+++liyaGaqKn+GpaG+t+vi
  lcl|FitnessBrowser__Pedo557:CA265_RS03895 138 QESAYIHYTSNNTIEGTEIFDFS-PNGVPVVCDMSSDIFSRKINVSDFDLIYAGAQKNMGPAGMTLVI 204
                                                99****************99765.6889**************************************** PP

                                  TIGR01364 206 vrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllY 273
                                                 +++ l++akke+ps++dY+i  +n s+yntpp+f+iyv+ l l wlk++GGv+ +e++n eKakllY
  lcl|FitnessBrowser__Pedo557:CA265_RS03895 205 AKNEFLNQAKKEIPSMMDYRIFRDNMSMYNTPPVFSIYVAMLNLLWLKDQGGVSGIEQRNIEKAKLLY 272
                                                ******************************************************************** PP

                                  TIGR01364 274 eaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpl 341
                                                  id++  ++ ++++ ++Rs+mnv+F   ++++e  Flk a+++g+v++kG+r+vGG+Ras+Ynalpl
  lcl|FitnessBrowser__Pedo557:CA265_RS03895 273 AEIDRNP-LFYGTADVAHRSRMNVTFLAVNKDVEGGFLKFAADQGIVGIKGYRTVGGFRASLYNALPL 339
                                                ****997.666889****************************************************** PP

                                  TIGR01364 342 eevqaLvdfmkeFekk 357
                                                 +v+ Lv+ m +Fek 
  lcl|FitnessBrowser__Pedo557:CA265_RS03895 340 SSVEVLVNAMASFEKI 355
                                                *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (365 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: 9.54
//
[ok]

This GapMind analysis is from Apr 09 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