Alignments for a candidate for dapC in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Desulfobacter vibrioformis DSM 8776

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_035236531.1 Q366_RS04025 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::Q59196
         (362 letters)



>NCBI__GCF_000745975.1:WP_035236531.1
          Length = 362

 Score =  395 bits (1015), Expect = e-115
 Identities = 205/359 (57%), Positives = 262/359 (72%), Gaps = 5/359 (1%)

Query: 3   KRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALL 62
           +R YNFNAGPAALPL VLE  QA F+++ ++GMSI E+SHR + ++ V N+A AR   LL
Sbjct: 4   QRIYNFNAGPAALPLPVLEEIQASFLNFGNSGMSITEISHRSSYFDDVINDAVARAKRLL 63

Query: 63  GNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVA-A 121
           G    Y VLFIQGGAS QFAMIPMNFL   Q+A+YV TG+W++KA+KEAK+    HV  A
Sbjct: 64  GLDDQYHVLFIQGGASLQFAMIPMNFLSGDQSADYVNTGTWSTKAIKEAKIQNKKHVVVA 123

Query: 122 SSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSR 181
           SSE  ++  +P    I    +A Y+H+TSN TI+G QF  FPDTG VP+I DMSSDI SR
Sbjct: 124 SSEDKDFSYIPG--NIPFSKDAKYVHITSNNTIKGTQFADFPDTGGVPIIADMSSDIFSR 181

Query: 182 PFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPP 241
           P  + +FG++YAGAQKNLGPSG  VVI+R+DL+  +   LP+ML+Y TY + NS+YNTPP
Sbjct: 182 PLPMEKFGMIYAGAQKNLGPSGTCVVILRKDLLETANSDLPSMLKYSTYAEKNSMYNTPP 241

Query: 242 SFGIYMVNEVLKWIEER-GGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNI 300
            FGIY ++ VLKWIEE  GGLE ++  N++KA L+YD ++ S  FYR      SRS MN+
Sbjct: 242 CFGIYTIDLVLKWIEEEMGGLEKMEAFNKEKAGLLYDFMEAS-NFYRATAAQGSRSLMNV 300

Query: 301 TFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKR 359
           TFRL SEELE++F+K +  +G  GLKGHRSVGG RASIYNA   E  +ALVQFM+ F++
Sbjct: 301 TFRLPSEELEQKFIKEATAKGLGGLKGHRSVGGCRASIYNATTMEGIKALVQFMDAFQK 359


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: 424
Number of extensions: 17
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: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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 WP_035236531.1 Q366_RS04025 (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.29776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-148  479.2   0.0   3.9e-148  479.1   0.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035236531.1  Q366_RS04025 3-phosphoserine/pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035236531.1  Q366_RS04025 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.1   0.0  3.9e-148  3.9e-148       1     357 [.       6     360 ..       6     361 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.1 bits;  conditional E-value: 3.9e-148
                                 TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 
                                               i+nF+aGPaalp  vle++q+ +l+f ++g+s++eisHRs+ f++v+++a    ++Ll + d+y+vlf+
  lcl|NCBI__GCF_000745975.1:WP_035236531.1   6 IYNFNAGPAALPLPVLEEIQASFLNFGNSGMSITEISHRSSYFDDVINDAVARAKRLLGLDDQYHVLFI 74 
                                               69******************************************************************* PP

                                 TIGR01364  70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138
                                               qGGa+ qfa++p+n+l+ ++ ady++tG+ws+ka+keak+  k+  vvas+e+k++s ip   ++ +++
  lcl|NCBI__GCF_000745975.1:WP_035236531.1  75 QGGASLQFAMIPMNFLSGDQSADYVNTGTWSTKAIKEAKIQNKKHVVVASSEDKDFSYIP--GNIPFSK 141
                                               *****************************************99888999999********..88999** PP

                                 TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207
                                               da+yv++++n+ti+G++f + p++  +p++aD+ssdi+sr++ ++k+g+iyaGaqKn+Gp+G +vvi+r
  lcl|NCBI__GCF_000745975.1:WP_035236531.1 142 DAKYVHITSNNTIKGTQFADFPDTGGVPIIADMSSDIFSRPLPMEKFGMIYAGAQKNLGPSGTCVVILR 210
                                               ********************************************************************* PP

                                 TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlke.kGGvkklekknqeKakllYea 275
                                               kdlle+a+++lps+l+Y++ ae++s+yntpp+f+iy+++lvlkw+ e  GG++k+e+ n+eKa llY+ 
  lcl|NCBI__GCF_000745975.1:WP_035236531.1 211 KDLLETANSDLPSMLKYSTYAEKNSMYNTPPCFGIYTIDLVLKWIEEeMGGLEKMEAFNKEKAGLLYDF 279
                                               *********************************************8626******************** PP

                                 TIGR01364 276 idesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleev 344
                                               +++s+ fy++++++ +Rslmnv+F+l++eele++F+kea++kgl +lkGhrsvGG+RasiYna ++e++
  lcl|NCBI__GCF_000745975.1:WP_035236531.1 280 MEASN-FYRATAAQGSRSLMNVTFRLPSEELEQKFIKEATAKGLGGLKGHRSVGGCRASIYNATTMEGI 347
                                               **997.*************************************************************** PP

                                 TIGR01364 345 qaLvdfmkeFekk 357
                                               +aLv+fm  F+k+
  lcl|NCBI__GCF_000745975.1:WP_035236531.1 348 KALVQFMDAFQKE 360
                                               **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (362 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.65
//
[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