Alignments for a candidate for dapC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Shewanella loihica PV-4

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 5209480 Shew_1950 phosphoserine aminotransferase (RefSeq)

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__PV4:5209480
          Length = 364

 Score =  406 bits (1043), Expect = e-118
 Identities = 208/364 (57%), Positives = 262/364 (71%), Gaps = 5/364 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M+  +NF +GPAMLP  V+++AQ+EL DWNG G SVME+SHR KEFI + E+AE D RDL
Sbjct: 1   MSATYNFCAGPAMLPQPVMQKAQEELLDWNGQGVSVMEISHRSKEFIALTEQAEADIRDL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           +N+PSNY VLF HGGGRGQFAAV  N+LG++  A Y+  G W+++A++EAKK       D
Sbjct: 61  MNIPSNYHVLFMHGGGRGQFAAVVNNLLGEQGKALYLVDGSWSSAAVEEAKKLAGDAQID 120

Query: 121 AKVTVD---GLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSS 177
               V+   G+  +      ++  +  Y+HYCPNET+DGI I E  +  +   + AD SS
Sbjct: 121 TLNIVEKTNGISRIVVPDLNEIKQDYRYLHYCPNETVDGIEIFE--EINSPWPIVADMSS 178

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
            I+SR IDVSRYG+IYAGAQKNIGP+GL+IVIVR+DLL    +   SI+DY +   + SM
Sbjct: 179 NIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDLLAYPQLTQASIMDYRLAVKHDSM 238

Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297
           FNTPPTFAWYL+  VFKWLKA GGVAE+ K+N +KAE LY  ID+ DFY N VA ANRS+
Sbjct: 239 FNTPPTFAWYLAAEVFKWLKAQGGVAEVAKVNDRKAETLYAYIDSGDFYENRVAVANRSK 298

Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357
           MNV F L D +L++ FL E+ AAGL ALKGHR VGGMRAS+YNAMPL GV+AL  FM  F
Sbjct: 299 MNVTFYLKDESLNEPFLAEAKAAGLVALKGHRSVGGMRASLYNAMPLVGVEALVSFMKAF 358

Query: 358 ERRH 361
             +H
Sbjct: 359 AEKH 362


Lambda     K      H
   0.319    0.136    0.405 

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: 394
Number of extensions: 13
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: 362
Length of database: 364
Length adjustment: 29
Effective length of query: 333
Effective length of database: 335
Effective search space:   111555
Effective search space used:   111555
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 5209480 Shew_1950 (phosphoserine aminotransferase (RefSeq))
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.5875.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.8e-152  491.9   0.0   5.4e-152  491.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209480  Shew_1950 phosphoserine aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209480  Shew_1950 phosphoserine aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.7   0.0  5.4e-152  5.4e-152       2     358 .]       5     362 ..       4     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 491.7 bits;  conditional E-value: 5.4e-152
                        TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfaa 79 
                                      +nF+aGPa+lp+ v++kaq+elld+ng+g+svmeisHRskef +++e+ae d+r+L+nip+ny+vlf+ GG+++qfaa
  lcl|FitnessBrowser__PV4:5209480   5 YNFCAGPAMLPQPVMQKAQEELLDWNGQGVSVMEISHRSKEFIALTEQAEADIRDLMNIPSNYHVLFMHGGGRGQFAA 82 
                                      8***************************************************************************** PP

                        TIGR01364  80 vplnllkekkvadyivtGawskkalkeakkltk..evkvvase.eekkyskipdeeelelkedaayvylcanetieGv 154
                                      v  nll e+ +a y+v G+ws+ a++eakkl    ++++++   +++  s+i   +  e+k+d+ y+++c net++G+
  lcl|FitnessBrowser__PV4:5209480  83 VVNNLLGEQGKALYLVDGSWSSAAVEEAKKLAGdaQIDTLNIVeKTNGISRIVVPDLNEIKQDYRYLHYCPNETVDGI 160
                                      *******************************9877666555443778899999999999******************* PP

                        TIGR01364 155 efkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaends 232
                                      e+ e+  ++  p+vaD+ss+i+sr+idvs+ygliyaGaqKniGp+G+++vivr+dll+  + + +s++dY+ ++++ds
  lcl|FitnessBrowser__PV4:5209480 161 EIFEEI-NSPWPIVADMSSNIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDLLAYPQLTQASIMDYRLAVKHDS 237
                                      ***999.789******************************************************************** PP

                        TIGR01364 233 lyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeF 310
                                      ++ntpptfa+y+++ v+kwlk++GGv++++k n +Ka+ lY +id+  +fy+n+v+ ++Rs+mnv+F lk+e l++ F
  lcl|FitnessBrowser__PV4:5209480 238 MFNTPPTFAWYLAAEVFKWLKAQGGVAEVAKVNDRKAETLYAYIDSG-DFYENRVAVANRSKMNVTFYLKDESLNEPF 314
                                      *********************************************65.6***************************** PP

                        TIGR01364 311 lkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                      l+ea+++glv+lkGhrsvGG+Ras+Yna+pl +v+aLv+fmk F++kh
  lcl|FitnessBrowser__PV4:5209480 315 LAEAKAAGLVALKGHRSVGGMRASLYNAMPLVGVEALVSFMKAFAEKH 362
                                      *********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (364 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: 7.71
//
[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