Alignments for a candidate for serC in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Nitriliruptor alkaliphilus DSM 45188

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_052667489.1 NITAL_RS17575 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_000969705.1:WP_052667489.1
          Length = 372

 Score =  405 bits (1041), Expect = e-118
 Identities = 202/374 (54%), Positives = 272/374 (72%), Gaps = 5/374 (1%)

Query: 5   LTPHLEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSG 64
           + P L IP  + P DGRFG GPSK+R E ++ L   A+ L GTSHR+  VK  V R++ G
Sbjct: 1   MAPDLTIPDDLLPADGRFGCGPSKIRPEAVERLAEVASDLLGTSHRKPAVKGQVQRLQEG 60

Query: 65  LAELFSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGE 124
           L+ LF LP+GYEV++  GGATAFWDAAAFGL+++RS H ++GEFS+KFA A +  P++ +
Sbjct: 61  LSGLFGLPEGYEVLVTLGGATAFWDAAAFGLVEQRSRHYSFGEFSSKFAKATAAAPWLSD 120

Query: 125 PIIITSDPGSAPEPQTDPS-VDVIAWAHNETSTGVAVAVRRPEGSDDALVVIDATSGAGG 183
           P +++++PG+ P     P+ VDV A+ HNETSTGV   ++ P  +DDALV++DATSGAGG
Sbjct: 121 PDVVSAEPGTRPTASAAPADVDVQAFTHNETSTGV---MQDPVRTDDALVLVDATSGAGG 177

Query: 184 LPVDIAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVEN 243
           LPVD+ +TD YYF+ QK FAS+GGL +A++SPAA+ RIEAIAA+ R+VP FL L  A+ N
Sbjct: 178 LPVDLTQTDVYYFSLQKGFASEGGLTVALVSPAAVQRIEAIAASDRYVPTFLDLSTALSN 237

Query: 244 SLKNQTYNTPAIATLALLAEQIDWLVGN-GGLDWAVKRTADSSQRLYSWAQERPYTTPFV 302
           + ++QTYNTP+++T+ L AEQ+DW+    GGLD  V    + +  +Y WA +R + +PFV
Sbjct: 238 ARQHQTYNTPSVSTVFLAAEQVDWMRATFGGLDGVVAAQREKAAHVYGWANDRAWASPFV 297

Query: 303 TDPGLRSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDV 362
           T+   RS VV TID  D V A  V  +LRANG++DT+ YRKLGRNQLR+ MFPAV+  D+
Sbjct: 298 TEDAARSLVVATIDLDDSVPADDVNAVLRANGVLDTDAYRKLGRNQLRIGMFPAVDAADL 357

Query: 363 SALTECVDWVVERL 376
            A T  VDWVVERL
Sbjct: 358 QAYTASVDWVVERL 371


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: 454
Number of extensions: 11
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: 376
Length of database: 372
Length adjustment: 30
Effective length of query: 346
Effective length of database: 342
Effective search space:   118332
Effective search space used:   118332
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_052667489.1 NITAL_RS17575 (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.24589.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-160  520.5   3.3   1.4e-160  520.3   3.3    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052667489.1  NITAL_RS17575 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052667489.1  NITAL_RS17575 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.3   3.3  1.4e-160  1.4e-160       2     361 .]      13     371 ..      12     371 .. 0.98

  Alignments for each domain:
  == domain 1  score: 520.3 bits;  conditional E-value: 1.4e-160
                                 TIGR01366   2 padgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggat 70 
                                               padgrfg+gpsk+r+e+++ l++ a+ llgtshr++avk  v +++egl+ lf lp+gyev++++ggat
  lcl|NCBI__GCF_000969705.1:WP_052667489.1  13 PADGRFGCGPSKIRPEAVERLAEVASDLLGTSHRKPAVKGQVQRLQEGLSGLFGLPEGYEVLVTLGGAT 81 
                                               9******************************************************************** PP

                                 TIGR01366  71 afwdaatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqae.egvdvialahne 138
                                               afwdaa+fgl+e++s+h sfgefsskfaka+  ap+l++p +v+a+pg+ p a a  + vdv a++hne
  lcl|NCBI__GCF_000969705.1:WP_052667489.1  82 AFWDAAAFGLVEQRSRHYSFGEFSSKFAKATAAAPWLSDPDVVSAEPGTRPTASAApADVDVQAFTHNE 150
                                               ***************************************************99876267********** PP

                                 TIGR01366 139 tstgvavavrrpegsdealvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaalerie 207
                                               tstgv+     p  +d+alv++datsgagglpvd+++tdvyyf+ qk fas+ggl +a++spaa++rie
  lcl|NCBI__GCF_000969705.1:WP_052667489.1 151 TSTGVMQD---PVRTDDALVLVDATSGAGGLPVDLTQTDVYYFSLQKGFASEGGLTVALVSPAAVQRIE 216
                                               *****965...55579***************************************************** PP

                                 TIGR01366 208 kiaasgrfvpeflslptavdnslknqtyntpavatlllldeqvdwlngn.ggldfavartkdsssrlys 275
                                               +iaas+r+vp fl+l ta+ n+++ qtyntp+v+t++l +eqvdw+ +  ggld++va  ++ + ++y 
  lcl|NCBI__GCF_000969705.1:WP_052667489.1 217 AIAASDRYVPTFLDLSTALSNARQHQTYNTPSVSTVFLAAEQVDWMRATfGGLDGVVAAQREKAAHVYG 285
                                               **********************************************8654******************* PP

                                 TIGR01366 276 waeereyatpfvadaakrsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidp 344
                                               wa++r  a+pfv++ a rs+vv tid++d++ a  v  +lrang++dt+ yrklgrnqlr++mfpa+d+
  lcl|NCBI__GCF_000969705.1:WP_052667489.1 286 WANDRAWASPFVTEDAARSLVVATIDLDDSVPADDVNAVLRANGVLDTDAYRKLGRNQLRIGMFPAVDA 354
                                               ********************************************************************* PP

                                 TIGR01366 345 advealteavdfvvekl 361
                                               ad++a t +vd+vve+l
  lcl|NCBI__GCF_000969705.1:WP_052667489.1 355 ADLQAYTASVDWVVERL 371
                                               ***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (372 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: 7.89
//
[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