Alignments for a candidate for serC in Azorhizobium caulinodans ORS 571

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Azorhizobium caulinodans ORS 571

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_012169515.1 AZC_RS05045 phosphoserine transaminase

Query= SwissProt::P52878
         (370 letters)



>NCBI__GCF_000010525.1:WP_012169515.1
          Length = 391

 Score =  487 bits (1254), Expect = e-142
 Identities = 235/378 (62%), Positives = 281/378 (74%), Gaps = 10/378 (2%)

Query: 3   PTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDD 62
           P + P NP FSSGPCAK PG+S++ L+D P GRSHR+ +GK KL  AI  TRD+L +PDD
Sbjct: 7   PHQKPANPNFSSGPCAKRPGWSLDALRDAPLGRSHRAKVGKAKLKLAIDLTRDVLEVPDD 66

Query: 63  YLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYG 122
           Y +GIVPASDTGA EM LWSMLG RGVD+L WESF +GW TD+ KQLKL++VR   A YG
Sbjct: 67  YRIGIVPASDTGAVEMVLWSMLGARGVDMLAWESFGEGWVTDVAKQLKLENVRTLTAPYG 126

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLD 182
           +LPDLK V+F+NDVVF WNGTTSGV VP+ DWIP +R GLT+CDATSA FA  + + KLD
Sbjct: 127 ELPDLKAVNFENDVVFTWNGTTSGVMVPDADWIPADRAGLTICDATSAAFAQPLDFAKLD 186

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGSTI 242
           V+TFSWQKVLGGE AHGMLILSPRAV+RLE+Y PAWPLPKIFR+TKGGKL + IFEG TI
Sbjct: 187 VVTFSWQKVLGGEAAHGMLILSPRAVERLETYKPAWPLPKIFRMTKGGKLIEGIFEGETI 246

Query: 243 NTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSML  ED++  L WA+SVGGL  L +R N N  V   +V +  W+ FLA     RS+
Sbjct: 247 NTPSMLCVEDYIDALHWAKSVGGLPGLKERANRNFEVIAQWVHRTPWVDFLATDPVTRSN 306

Query: 303 TSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352
           TSVC KV          D      K +   LEK  +AYDIGSYRDAP+GLRIWCGATV+ 
Sbjct: 307 TSVCLKVVDPAVTTLPADAQAAFAKAITSGLEKGDIAYDIGSYRDAPAGLRIWCGATVQA 366

Query: 353 EDLQCLCEWIEWAYNLVK 370
            D++ L  W++WA+ + K
Sbjct: 367 TDIEALTHWLDWAFTVAK 384


Lambda     K      H
   0.318    0.136    0.429 

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: 523
Number of extensions: 23
Number of successful extensions: 2
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: 391
Length adjustment: 30
Effective length of query: 340
Effective length of database: 361
Effective search space:   122740
Effective search space used:   122740
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_012169515.1 AZC_RS05045 (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.2135131.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-215  699.3   1.1     7e-215  699.1   1.1    1.0  1  NCBI__GCF_000010525.1:WP_012169515.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012169515.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.1   1.1    7e-215    7e-215       1     373 [.      10     382 ..      10     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 699.1 bits;  conditional E-value: 7e-215
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           +panp+fssgpcakrpg+s+++l++a+lgrshr+k+gk+klk ai+ tr+vlevp+dy+igiv+asdtgavem
  NCBI__GCF_000010525.1:WP_012169515.1  10 KPANPNFSSGPCAKRPGWSLDALRDAPLGRSHRAKVGKAKLKLAIDLTRDVLEVPDDYRIGIVPASDTGAVEM 82 
                                           69*********************************************************************** PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           +lws+lgargvd+la+esfg+gwvtdv+kqlkl++vr l a+yg+lpdlk v+f++dvvftwngttsgv vp+
  NCBI__GCF_000010525.1:WP_012169515.1  83 VLWSMLGARGVDMLAWESFGEGWVTDVAKQLKLENVRTLTAPYGELPDLKAVNFENDVVFTWNGTTSGVMVPD 155
                                           ************************************************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           +d+ipadr glticdatsaafaq ld+ kldvvtfswqkvlgge ahg+lilsprav+rle+y+pawplpkif
  NCBI__GCF_000010525.1:WP_012169515.1 156 ADWIPADRAGLTICDATSAAFAQPLDFAKLDVVTFSWQKVLGGEAAHGMLILSPRAVERLETYKPAWPLPKIF 228
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           r+tkggkl+++ifegetintpsml+ved++dal+wa+s+ggl  l +ra+ n +v++++v +++wvdfla+ +
  NCBI__GCF_000010525.1:WP_012169515.1 229 RMTKGGKLIEGIFEGETINTPSMLCVEDYIDALHWAKSVGGLPGLKERANRNFEVIAQWVHRTPWVDFLATDP 301
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                            +rsntsvclkvvdp+v++l++daqa fak + s lek ++aydigsyrdapaglriwcgatv++ d+eal++
  NCBI__GCF_000010525.1:WP_012169515.1 302 VTRSNTSVCLKVVDPAVTTLPADAQAAFAKAITSGLEKGDIAYDIGSYRDAPAGLRIWCGATVQATDIEALTH 374
                                           ************************************************************************* PP

                             TIGR01365 366 wldwafal 373
                                           wldwaf++
  NCBI__GCF_000010525.1:WP_012169515.1 375 WLDWAFTV 382
                                           ******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (391 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: 17.71
//
[ok]

This GapMind analysis is from Jul 25 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 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