Alignments for a candidate for dapC in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Bacteroides thetaiotaomicron VPI-5482

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate 350681 BT1153 phosphoserine aminotransferase (NCBI ptt file)

Query= SwissProt::Q59196
         (362 letters)



>FitnessBrowser__Btheta:350681
          Length = 355

 Score =  301 bits (772), Expect = 1e-86
 Identities = 160/359 (44%), Positives = 236/359 (65%), Gaps = 10/359 (2%)

Query: 4   RAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLG 63
           + +NFNAGP+ LP EV+E      +D+  +G+S+ME+SHR   ++ V +EA+A    LL 
Sbjct: 2   KKHNFNAGPSILPREVIEDTAKAILDFNGSGLSLMEISHRAKDFQPVVDEAEALFKELLN 61

Query: 64  NPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASS 123
            P GY VLF+ GGAS +F M+P NFL++   A Y+ TG WA KA+KEAK  G+    ASS
Sbjct: 62  IPEGYSVLFLGGGASMEFCMVPFNFLEK--KAAYLNTGVWAKKAMKEAKGFGEVVEVASS 119

Query: 124 EASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGS-VPLIGDMSSDILSRP 182
             + Y  +PK  +  +  +A Y H+T+N TI G + K   D  S VP++ DMSSDI SRP
Sbjct: 120 AEATYTYIPK--DYTIPADADYFHITTNNTIYGTELKE--DLNSPVPMVADMSSDIFSRP 175

Query: 183 FDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPS 242
            D++++  +Y GAQKNL P+GVT VIV+ D V +  +++P+ML Y T++ N S++NTPP 
Sbjct: 176 IDVSKYICIYGGAQKNLAPAGVTFVIVKNDAVGKVSRYIPSMLNYQTHIDNGSMFNTPPV 235

Query: 243 FGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITF 302
             IY     L+WI+ +GG++ +++   +KA ++Y  ID++  F  G    + RS MNI F
Sbjct: 236 VPIYAALLNLRWIKAQGGVKEMERRAIEKADMLYAEIDRNKLFV-GTAAKEDRSRMNICF 294

Query: 303 RLASE--ELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKR 359
            +A E  +LE +F+K + ++G VG+KGHRSVGG RAS YNA+P ES +AL+  M+ F++
Sbjct: 295 VMAPEYKDLEADFMKFATEKGMVGIKGHRSVGGFRASCYNALPKESVQALIDCMQEFEK 353


Lambda     K      H
   0.316    0.132    0.378 

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: 335
Number of extensions: 21
Number of successful extensions: 5
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: 362
Length of database: 355
Length adjustment: 29
Effective length of query: 333
Effective length of database: 326
Effective search space:   108558
Effective search space used:   108558
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 350681 BT1153 (phosphoserine aminotransferase (NCBI ptt file))
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.22531.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.1e-139  449.4   0.0   4.6e-139  449.2   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350681  BT1153 phosphoserine aminotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350681  BT1153 phosphoserine aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.2   0.0  4.6e-139  4.6e-139       2     358 .]       4     355 .]       3     355 .] 0.97

  Alignments for each domain:
  == domain 1  score: 449.2 bits;  conditional E-value: 4.6e-139
                          TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqf 77 
                                        +nF+aGP++lp+ev+e+ +k +ldfng+gls+meisHR+k+f+ vv+eae  ++eLlnip+ y+vlfl GGa+ +f
  lcl|FitnessBrowser__Btheta:350681   4 HNFNAGPSILPREVIEDTAKAILDFNGSGLSLMEISHRAKDFQPVVDEAEALFKELLNIPEGYSVLFLGGGASMEF 79 
                                        8*************************************************************************** PP

                          TIGR01364  78 aavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcanetieG 153
                                         +vp+n+l++k  a+y++tG+w+kka+keak +++ v  vas++e  y+ ip  +++++  da+y+++++n+ti+G
  lcl|FitnessBrowser__Btheta:350681  80 CMVPFNFLEKK--AAYLNTGVWAKKAMKEAKGFGE-VVEVASSAEATYTYIP--KDYTIPADADYFHITTNNTIYG 150
                                        ********988..********************99.66677777899*****..8899999*************** PP

                          TIGR01364 154 vefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilae 229
                                        +e ke   ++ +p+vaD+ssdi+sr+idvsky  iy+GaqKn+ paGvt+viv++d +++ ++ +ps+l+Y+++++
  lcl|FitnessBrowser__Btheta:350681 151 TELKEDL-NSPVPMVADMSSDIFSRPIDVSKYICIYGGAQKNLAPAGVTFVIVKNDAVGKVSRYIPSMLNYQTHID 225
                                        ****999.789***************************************************************** PP

                          TIGR01364 230 ndslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkke. 304
                                        n s++ntpp++ iy++ l l+w+k++GGvk++e++  eKa++lY  id++ +++ ++++k++Rs+mn++F ++ e 
  lcl|FitnessBrowser__Btheta:350681 226 NGSMFNTPPVVPIYAALLNLRWIKAQGGVKEMERRAIEKADMLYAEIDRN-KLFVGTAAKEDRSRMNICFVMAPEy 300
                                        ************************************************87.6********************9988 PP

                          TIGR01364 305 .elekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                         +le+ F+k a+ekg+v++kGhrsvGG+Ras Ynalp e+vqaL+d m+eFek h
  lcl|FitnessBrowser__Btheta:350681 301 kDLEADFMKFATEKGMVGIKGHRSVGGFRASCYNALPKESVQALIDCMQEFEKLH 355
                                        8***************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (355 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: 6.76
//
[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