Alignments for a candidate for serC in Methylobacterium sp. 4-46

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Methylobacterium sp. 4-46

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_012336037.1 M446_RS30960 phosphoserine transaminase

Query= metacyc::MONOMER-15918
         (370 letters)



>NCBI__GCF_000019365.1:WP_012336037.1
          Length = 390

 Score =  442 bits (1136), Expect = e-129
 Identities = 219/376 (58%), Positives = 267/376 (71%), Gaps = 12/376 (3%)

Query: 2   KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61
           +P   P+ P FSSGPCAK PG++   L D   GRSHR+K GK KL +AI  TR +L +PD
Sbjct: 4   RPDARPRAPFFSSGPCAKRPGWTPAALSDAALGRSHRAKLGKAKLKQAIDLTRTVLQVPD 63

Query: 62  DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121
           DY +GIVPASDTGA EM +WS+LG R V++L WESF +GW TD  KQL+L D RV  A Y
Sbjct: 64  DYRIGIVPASDTGAVEMAMWSLLGPRPVEMLAWESFGEGWVTDAVKQLRL-DARVTTAPY 122

Query: 122 GKLPDLKKVDFKN-DVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHK 180
           G LPDL  VD ++ DVVF WNGTTSGV+VP+ADWI  DREGV +CDATSA FA D+ + K
Sbjct: 123 GALPDLAAVDTRHHDVVFTWNGTTSGVRVPDADWIAADREGVVICDATSAAFAQDLDWAK 182

Query: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGS 240
           LD +TFSWQKVLGGE AHGMLILSPRA  RLES+ PAWP+PKIFR+TKGGKL + +F G 
Sbjct: 183 LDAVTFSWQKVLGGEAAHGMLILSPRAAARLESHVPAWPMPKIFRMTKGGKLIEGLFEGE 242

Query: 241 TINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIR 300
           TINTPSMLA ED++  L WA+ +GGL  L  R + N  V  A+VA+  W+  LA      
Sbjct: 243 TINTPSMLAVEDYIDALLWAQGIGGLPALRARADANARVIAAWVARTPWVENLARAPATA 302

Query: 301 SSTSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATV 350
           S+TSVC  +          +      K +  TLE+E VA D+G+YRDAP+GLRIWCGATV
Sbjct: 303 SNTSVCLVIADPEVTGRGPEAVAALAKGIAATLEREGVALDVGAYRDAPAGLRIWCGATV 362

Query: 351 EKEDLECLCEWIEWAY 366
           E+ DLE L  W++WA+
Sbjct: 363 ERSDLEALTPWLDWAF 378


Lambda     K      H
   0.319    0.136    0.430 

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: 489
Number of extensions: 18
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: 370
Length of database: 390
Length adjustment: 30
Effective length of query: 340
Effective length of database: 360
Effective search space:   122400
Effective search space used:   122400
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_012336037.1 M446_RS30960 (phosphoserine transaminase)
to HMM TIGR01365 (phosphoserine aminotransferase (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/TIGR01365.hmm
# target sequence database:        /tmp/gapView.8683.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01365  [M=374]
Accession:   TIGR01365
Description: serC_2: phosphoserine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-199  646.6   1.3   7.5e-199  646.4   1.3    1.0  1  lcl|NCBI__GCF_000019365.1:WP_012336037.1  M446_RS30960 phosphoserine trans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019365.1:WP_012336037.1  M446_RS30960 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.4   1.3  7.5e-199  7.5e-199       1     373 [.       8     380 ..       8     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: 646.4 bits;  conditional E-value: 7.5e-199
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               rp  p fssgpcakrpg+++ +l +aalgrshr+klgk+klk+ai+ tr vl+vp+dy+igiv+asdtg
  lcl|NCBI__GCF_000019365.1:WP_012336037.1   8 RPRAPFFSSGPCAKRPGWTPAALSDAALGRSHRAKLGKAKLKQAIDLTRTVLQVPDDYRIGIVPASDTG 76 
                                               6999***************************************************************** PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdf.kkdvvftwng 137
                                               avema+wsllg r+v++la+esfg+gwvtd +kql+l d rv  a+yg lpdl+ vd  ++dvvftwng
  lcl|NCBI__GCF_000019365.1:WP_012336037.1  77 AVEMAMWSLLGPRPVEMLAWESFGEGWVTDAVKQLRL-DARVTTAPYGALPDLAAVDTrHHDVVFTWNG 144
                                               ************************************9.89*****************8357******** PP

                                 TIGR01365 138 ttsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarl 206
                                               ttsgvrvp++d+i+adreg+ icdatsaafaqdld+ kld vtfswqkvlgge ahg+lilspra arl
  lcl|NCBI__GCF_000019365.1:WP_012336037.1 145 TTSGVRVPDADWIAADREGVVICDATSAAFAQDLDWAKLDAVTFSWQKVLGGEAAHGMLILSPRAAARL 213
                                               ********************************************************************* PP

                                 TIGR01365 207 esytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavl 275
                                               es+ pawp+pkifr+tkggkl++++fegetintpsmlaved++dal wa+ iggl al arad+n++v+
  lcl|NCBI__GCF_000019365.1:WP_012336037.1 214 ESHVPAWPMPKIFRMTKGGKLIEGLFEGETINTPSMLAVEDYIDALLWAQGIGGLPALRARADANARVI 282
                                               ********************************************************************* PP

                                 TIGR01365 276 eafvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdap 344
                                               +a+va+++wv+ la  +++ sntsvcl ++dp+v+    +a a +ak+++ +le+egva+d+g+yrdap
  lcl|NCBI__GCF_000019365.1:WP_012336037.1 283 AAWVARTPWVENLARAPATASNTSVCLVIADPEVTGRGPEAVAALAKGIAATLEREGVALDVGAYRDAP 351
                                               ********************************************************************* PP

                                 TIGR01365 345 aglriwcgatveksdleallewldwafal 373
                                               aglriwcgatve+sdleal++wldwafa 
  lcl|NCBI__GCF_000019365.1:WP_012336037.1 352 AGLRIWCGATVERSDLEALTPWLDWAFAQ 380
                                               ***************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (390 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.55
//
[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