Alignments for a candidate for serB in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Haloechinothrix alba DSM 45207

Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate WP_089302872.1 CHB84_RS18320 phosphoserine phosphatase SerB

Query= BRENDA::O53289
         (409 letters)



>NCBI__GCF_900188115.1:WP_089302872.1
          Length = 413

 Score =  463 bits (1192), Expect = e-135
 Identities = 251/402 (62%), Positives = 307/402 (76%), Gaps = 15/402 (3%)

Query: 7   VLITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGRLTLGVLVSCPLDVADGTALRD 66
           VLIT TG D+PGV+SALF VL +H V++L+VEQVVIRG+L LGVLV       D  AL++
Sbjct: 6   VLITTTGPDKPGVSSALFAVLTRHDVDVLDVEQVVIRGQLVLGVLVDVD---NDPEALQE 62

Query: 67  DVAAAIHGVGLDVAIERSDDL---PII--RQPSTHTIFVLGRPITAGAFSAVARGVAALG 121
            V  A+  V + V +    ++   P    R  S+H + VLGRP+TA AFS VAR +A L 
Sbjct: 63  SVEQAMATVAMRVDVRIGSEIGDDPFAPGRSDSSHVVVVLGRPVTARAFSEVARRLAVLD 122

Query: 122 VNIDFIRGISDYPVTGLELRVSVPPGCVG-------PLQIALTKVAAEEHVDVAVEDYGL 174
           VNID IRG++DYPVTGLE+ +S P    G        L+ AL  V+A+E+VD+AVE  GL
Sbjct: 123 VNIDSIRGVADYPVTGLEMHISAPDSAEGNGVQSDADLREALADVSAKENVDIAVEREGL 182

Query: 175 AWRTKRLIVFDVDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGELDFAESLQRRVATL 234
           A R KRL+VFDVDSTL++GEVIEMLAA AG + +VA ITEAAMRGEL+F ESL+RRVA L
Sbjct: 183 ARRAKRLVVFDVDSTLIRGEVIEMLAAHAGVEDEVARITEAAMRGELNFTESLERRVALL 242

Query: 235 AGLPATVIDDVAEQLELMPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDFVAS 294
            GLP + +D+VA+ + L PGARTTIRTL+RLGFRCGVVSGGF RII+ L  EL LDF+A+
Sbjct: 243 RGLPESALDEVADAITLTPGARTTIRTLKRLGFRCGVVSGGFTRIIQGLGDELGLDFIAA 302

Query: 295 NELEIVDGILTGRVVGPIVDRPGKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAGL 354
           NELEIVDG +TGRV+G  +DR GKA+AL  FA +Y +P+ Q+VAVGDGANDIDML AAG+
Sbjct: 303 NELEIVDGTITGRVLGEPIDRAGKARALERFADEYEIPLTQSVAVGDGANDIDMLSAAGM 362

Query: 355 GIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIEAADA 396
           G+AFNAKPALREVAD SLS+PYLD VLF++GVTR EIEAADA
Sbjct: 363 GVAFNAKPALREVADTSLSYPYLDAVLFMMGVTRAEIEAADA 404


Lambda     K      H
   0.321    0.139    0.395 

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: 541
Number of extensions: 24
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: 409
Length of database: 413
Length adjustment: 31
Effective length of query: 378
Effective length of database: 382
Effective search space:   144396
Effective search space used:   144396
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_089302872.1 CHB84_RS18320 (phosphoserine phosphatase SerB)
to HMM TIGR00338 (serB: phosphoserine phosphatase SerB (EC 3.1.3.3))

# 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/TIGR00338.hmm
# target sequence database:        /tmp/gapView.24585.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00338  [M=219]
Accession:   TIGR00338
Description: serB: phosphoserine phosphatase SerB
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-78  247.7   0.0    6.9e-78  247.2   0.0    1.2  1  lcl|NCBI__GCF_900188115.1:WP_089302872.1  CHB84_RS18320 phosphoserine phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089302872.1  CHB84_RS18320 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.2   0.0   6.9e-78   6.9e-78       2     217 ..     175     390 ..     174     392 .. 0.97

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 6.9e-78
                                 TIGR00338   2 iakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllk 70 
                                               ia++ +   +++k+lvvfD+Dstli+ EvI+ +a+ aGve+eV++iTe Amrgel+F+esl+ Rv+ll+
  lcl|NCBI__GCF_900188115.1:WP_089302872.1 175 IAVEREGLARRAKRLVVFDVDSTLIRGEVIEMLAAHAGVEDEVARITEAAMRGELNFTESLERRVALLR 243
                                               566666677899********************************************************* PP

                                 TIGR00338  71 glpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkl 139
                                               glp++ l++v++ ++lt+G++ ++++Lk+ g++  v+SGgF+ +++ l ++Lgld+++aN+Le+ dg +
  lcl|NCBI__GCF_900188115.1:WP_089302872.1 244 GLPESALDEVADAITLTPGARTTIRTLKRLGFRCGVVSGGFTRIIQGLGDELGLDFIAANELEIVDGTI 312
                                               ********************************************************************* PP

                                 TIGR00338 140 tGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivie 208
                                               tG+v ge++d   ka+ l++ + +++i+l+++vavGDGanD+ m++aAg+g+afnakp+l+e+ad++++
  lcl|NCBI__GCF_900188115.1:WP_089302872.1 313 TGRVLGEPIDRAGKARALERFADEYEIPLTQSVAVGDGANDIDMLSAAGMGVAFNAKPALREVADTSLS 381
                                               ********************************************************************* PP

                                 TIGR00338 209 kkdltdile 217
                                                 +l ++l 
  lcl|NCBI__GCF_900188115.1:WP_089302872.1 382 YPYLDAVLF 390
                                               999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (413 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: 00:00:00.00
# Mc/sec: 15.19
//
[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