Alignments for a candidate for serC in Rhodanobacter denitrificans FW104-10B01

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Rhodanobacter denitrificans FW104-10B01

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_007508577.1 LRK54_RS00400 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_021560695.1:WP_007508577.1
          Length = 362

 Score =  377 bits (968), Expect = e-109
 Identities = 192/363 (52%), Positives = 248/363 (68%), Gaps = 2/363 (0%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M++++NFS+GPA LP  VL++AQ+E+ DWNG G SVME SHRGK FI +A +AE D R+L
Sbjct: 1   MSRVWNFSAGPAALPLAVLERAQREMLDWNGSGASVMEQSHRGKRFIAMAAQAEADLREL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           + +P++Y VLF  GG    FA +P+N+ G   +ADYV +G+W+A A  EA  Y   NV  
Sbjct: 61  MGIPADYAVLFLQGGATQHFAQIPMNLAGAGDSADYVVSGHWSAKAASEAGSYVRVNVA- 119

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
           A    DG   + P   W+L  +AAY+HY PNETI G+     PD G  V + AD SS IL
Sbjct: 120 ASSEADGYLRLPPRDSWRLDPHAAYVHYTPNETIHGVEFHAIPDVGGTVPLVADLSSNIL 179

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           S P+DVSR+G+IYAGAQKNIGP+GL ++I+R DLL +A      I  Y+      SM NT
Sbjct: 180 SEPLDVSRFGLIYAGAQKNIGPSGLVVLIIRRDLLQRAGRPMARIFRYAEHAAADSMLNT 239

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNS-DFYRNDVAKANRSRMN 299
           P T+ WY++GL F+WLKA GG+  M + N+ KAELLY  ID S  +YRN +  + RSRMN
Sbjct: 240 PNTWGWYVAGLTFQWLKAQGGLGTMAERNRLKAELLYQAIDGSGGYYRNPIEPSARSRMN 299

Query: 300 VPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFER 359
           V F L D ALD  FL+ES AAGL ALKGH+ +GGMRAS+YNA+P E V+AL  FM +F +
Sbjct: 300 VRFTLHDGALDAAFLQESEAAGLLALKGHKALGGMRASLYNAVPPEAVQALVAFMRDFAQ 359

Query: 360 RHG 362
           RHG
Sbjct: 360 RHG 362


Lambda     K      H
   0.319    0.136    0.405 

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: 392
Number of extensions: 16
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_007508577.1 LRK54_RS00400 (3-phosphoserine/phosphohydroxythreonine transaminase)
to HMM TIGR01364 (serC: phosphoserine transaminase (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/TIGR01364.hmm
# target sequence database:        /tmp/gapView.3909045.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01364  [M=358]
Accession:   TIGR01364
Description: serC_1: phosphoserine transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-153  495.9   0.0   3.2e-153  495.8   0.0    1.0  1  NCBI__GCF_021560695.1:WP_007508577.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_021560695.1:WP_007508577.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.8   0.0  3.2e-153  3.2e-153       2     358 .]       5     361 ..       4     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.8 bits;  conditional E-value: 3.2e-153
                             TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGat 74 
                                            nFsaGPaalp +vle+aq+e+ld+ng+g+svme sHR k+f +++ +ae dlreL+ ip +y+vlflqGGat
  NCBI__GCF_021560695.1:WP_007508577.1   5 WNFSAGPAALPLAVLERAQREMLDWNGSGASVMEQSHRGKRFIAMAAQAEADLRELMGIPADYAVLFLQGGAT 77 
                                           7************************************************************************ PP

                             TIGR01364  75 tqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylca 147
                                           + fa++p+nl+ +++ ady+v+G+ws+ka++ea  +++ v+v+as+e + y ++p +++++l+++aayv+++ 
  NCBI__GCF_021560695.1:WP_007508577.1  78 QHFAQIPMNLAGAGDSADYVVSGHWSAKAASEAGSYVR-VNVAASSEADGYLRLPPRDSWRLDPHAAYVHYTP 149
                                           ************************************99.********************************** PP

                             TIGR01364 148 netieGvefkelpevkk.aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelp 219
                                           neti+Gvef+ +p+v   +plvaDlss+ils+++dvs++gliyaGaqKniGp+G++v+i+r+dll+ra + ++
  NCBI__GCF_021560695.1:WP_007508577.1 150 NETIHGVEFHAIPDVGGtVPLVADLSSNILSEPLDVSRFGLIYAGAQKNIGPSGLVVLIIRRDLLQRAGRPMA 222
                                           **************98769****************************************************** PP

                             TIGR01364 220 svldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaR 292
                                            +++Y+ +a  ds++ntp t+++yv+gl+++wlk++GG+ +++++n+ Ka+llY+aid s g+y+n++e++aR
  NCBI__GCF_021560695.1:WP_007508577.1 223 RIFRYAEHAAADSMLNTPNTWGWYVAGLTFQWLKAQGGLGTMAERNRLKAELLYQAIDGSGGYYRNPIEPSAR 295
                                           ************************************************************************* PP

                             TIGR01364 293 slmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                           s+mnv Ftl++  l++ Fl+e+e++gl++lkGh+++GG+Ras+Yna+p e+vqaLv+fm++F+++h
  NCBI__GCF_021560695.1:WP_007508577.1 296 SRMNVRFTLHDGALDAAFLQESEAAGLLALKGHKALGGMRASLYNAVPPEAVQALVAFMRDFAQRH 361
                                           ***************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (362 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.40
//
[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