Alignments for a candidate for serC in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Amycolatopsis halophila YIM 93223

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_034268890.1 AMYHA_RS06245 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_000504245.1:WP_034268890.1
          Length = 375

 Score =  512 bits (1319), Expect = e-150
 Identities = 245/366 (66%), Positives = 292/366 (79%)

Query: 11  IPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAELFS 70
           IP  IKP DGRFG GPSKVR EQL  L +  A++ GTSHRQ PVK+LVGRVR GL ELFS
Sbjct: 9   IPDDIKPSDGRFGCGPSKVRPEQLANLASDGASVMGTSHRQKPVKSLVGRVREGLRELFS 68

Query: 71  LPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIIITS 130
           LP+GYEV+LGNGG TAFWDAAAFGL+ +R+ H TYGEFS+KFA   +  PF+ + I++  
Sbjct: 69  LPEGYEVVLGNGGTTAFWDAAAFGLVRERAQHFTYGEFSSKFAKVTNGAPFLADSIVVEG 128

Query: 131 DPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDDALVVIDATSGAGGLPVDIAE 190
           +PGSAP        D++ WAHNETSTGVAV VRRPEGS+ ALV IDATSGAGGLPV+  +
Sbjct: 129 EPGSAPAISYQQGADLVGWAHNETSTGVAVPVRRPEGSEGALVAIDATSGAGGLPVNAED 188

Query: 191 TDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKNQTY 250
            D YYFAPQK+FASDGGLWLA+MSPAA+ R+  I A+ RWVP+FLSL  A++NS K+QTY
Sbjct: 189 FDVYYFAPQKSFASDGGLWLALMSPAAIERVGEIGASDRWVPEFLSLTTALDNSRKDQTY 248

Query: 251 NTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGLRSQ 310
           NTPA+ATL LLA+Q+DW+  NGGL W  +RTA+SS RLY WA++  Y +PFVT+  LRSQ
Sbjct: 249 NTPALATLFLLADQLDWMNSNGGLKWTTERTAESSGRLYEWAEKTSYASPFVTETALRSQ 308

Query: 311 VVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTECVD 370
           VVGTIDF DD+DA  VAK LRAN IVD EPYRKLGRNQLRV  FPA+EPDDV+ LT C++
Sbjct: 309 VVGTIDFSDDIDAAAVAKTLRANNIVDVEPYRKLGRNQLRVGTFPAIEPDDVTKLTRCIE 368

Query: 371 WVVERL 376
           +VVE+L
Sbjct: 369 YVVEQL 374


Lambda     K      H
   0.317    0.134    0.399 

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: 507
Number of extensions: 8
Number of successful extensions: 1
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: 376
Length of database: 375
Length adjustment: 30
Effective length of query: 346
Effective length of database: 345
Effective search space:   119370
Effective search space used:   119370
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: 50 (23.9 bits)

Align candidate WP_034268890.1 AMYHA_RS06245 (phosphoserine transaminase)
to HMM TIGR01366 (putative 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/TIGR01366.hmm
# target sequence database:        /tmp/gapView.501609.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01366  [M=361]
Accession:   TIGR01366
Description: serC_3: putative 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-196  638.3   0.1   2.3e-196  638.1   0.1    1.0  1  NCBI__GCF_000504245.1:WP_034268890.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034268890.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  638.1   0.1  2.3e-196  2.3e-196       1     361 []      14     374 ..      14     374 .. 1.00

  Alignments for each domain:
  == domain 1  score: 638.1 bits;  conditional E-value: 2.3e-196
                             TIGR01366   1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggatafw 73 
                                           kp+dgrfg+gpskvr+eql  l++ +as++gtshrq +vk lvg+vregl+elfslp+gyev+lgngg+tafw
  NCBI__GCF_000504245.1:WP_034268890.1  14 KPSDGRFGCGPSKVRPEQLANLASDGASVMGTSHRQKPVKSLVGRVREGLRELFSLPEGYEVVLGNGGTTAFW 86 
                                           79*********************************************************************** PP

                             TIGR01366  74 daatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahnetstgvava 146
                                           daa+fgl+ ++++h+++gefsskfak ++ apfl++ ++v  +pgsap+   ++g+d++++ahnetstgvav+
  NCBI__GCF_000504245.1:WP_034268890.1  87 DAAAFGLVRERAQHFTYGEFSSKFAKVTNGAPFLADSIVVEGEPGSAPAISYQQGADLVGWAHNETSTGVAVP 159
                                           ************************************************************************* PP

                             TIGR01366 147 vrrpegsdealvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaaleriekiaasgrfvpef 219
                                           vrrpegs++alv+idatsgagglpv+ ++ dvyyfapqksfasdgglwla++spaa+er+ +i as+r+vpef
  NCBI__GCF_000504245.1:WP_034268890.1 160 VRRPEGSEGALVAIDATSGAGGLPVNAEDFDVYYFAPQKSFASDGGLWLALMSPAAIERVGEIGASDRWVPEF 232
                                           ************************************************************************* PP

                             TIGR01366 220 lslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlyswaeereyatpfvadaak 292
                                           lsl ta+dns+k+qtyntpa+atl+ll++q+dw+n+nggl ++++rt++ss rly+wae++ ya+pfv+++a+
  NCBI__GCF_000504245.1:WP_034268890.1 233 LSLTTALDNSRKDQTYNTPALATLFLLADQLDWMNSNGGLKWTTERTAESSGRLYEWAEKTSYASPFVTETAL 305
                                           ************************************************************************* PP

                             TIGR01366 293 rsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpadvealteavdfvvekl 361
                                           rsqvvgtidfsddidaa+vak lran ivd epyrklgrnqlrv+ fpai+p+dv +lt+++++vve+l
  NCBI__GCF_000504245.1:WP_034268890.1 306 RSQVVGTIDFSDDIDAAAVAKTLRANNIVDVEPYRKLGRNQLRVGTFPAIEPDDVTKLTRCIEYVVEQL 374
                                           ******************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (375 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.21
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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