Alignments for a candidate for serC in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Dyella japonica UNC79MFTsu3.2

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate N515DRAFT_1430 N515DRAFT_1430 phosphoserine aminotransferase apoenzyme

Query= BRENDA::Q96255
         (430 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1430
          Length = 361

 Score =  380 bits (976), Expect = e-110
 Identities = 184/358 (51%), Positives = 254/358 (70%)

Query: 72  RVFNFAAGPATLPENVLLKAQADLYNWRGSGMSVMEMSHRGKEFLSIIQKAESDLRQLLE 131
           RV+NF+AGPA +P  VL +AQ +L +W GSG SVME+SHRGK F+ + ++AE+DLR+LL+
Sbjct: 3   RVWNFSAGPAAIPTAVLERAQRELLDWNGSGASVMELSHRGKRFIGLAEQAEADLRELLK 62

Query: 132 IPQEYSVLFLQGGATTQFAALPLNLCKSDDTVDFVVTGSWGDKAVKEAKKYCKTNVIWSG 191
           IP +Y+VLFLQGGAT  FA +PLNL    D+ D++V G WG+KA  EA  Y + NV  S 
Sbjct: 63  IPADYAVLFLQGGATQHFAQIPLNLAGEGDSADYIVNGHWGEKAASEAASYVRVNVAASS 122

Query: 192 KSEKYTKVPSFEELEQTPDAKYLHICANETIHGVEFKDYPVPKNGFLVADMSSNFCSKPV 251
           ++E+Y ++P     +  P A Y+H   NETIHGVE+ D P      LVADMSSN  ++P+
Sbjct: 123 RNEQYLRLPPRASWQLDPRAAYVHYTPNETIHGVEYHDVPEVGEVPLVADMSSNILAEPL 182

Query: 252 DVSKFGVIYGGAQKNVGPSGVTIVIIRKDLIGNAQDITPVMLDYKIHDENSSLYNTPPCF 311
           DVS+FG+IY GAQKN+GPSG+ ++IIR+DL+  A      +  Y  H  N S+ NTP  +
Sbjct: 183 DVSRFGLIYAGAQKNIGPSGLVVMIIRRDLLQRAARPMAKIFRYAEHAANDSMLNTPNTW 242

Query: 312 GIYMCGLVFEDLLEQGGLKEVEKKNQRKADLLYNAIEESNGFFRCPVEKSVRSLMNVPFT 371
           G Y+ GL F+ L EQGGL+ +  +N+ KA LLY AI+ S G++R P++ + RS MNVPFT
Sbjct: 243 GWYLAGLTFQWLKEQGGLEAMAHRNRDKAGLLYQAIDGSGGYYRNPIDPAARSRMNVPFT 302

Query: 372 LEKSELEAEFIKEAAKEKMVQLKGHRSVGGMRASIYNAMPLAGVEKLVAFMKDFQAKH 429
           L  S L+A+F+KE+    ++ LKGH+++GGMRAS+YNA+PL  V+ LV FM+DF A+H
Sbjct: 303 LHDSALDADFLKESEAAGLLALKGHKALGGMRASLYNAVPLEAVQVLVQFMRDFAARH 360


Lambda     K      H
   0.316    0.132    0.381 

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: 362
Number of extensions: 10
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: 430
Length of database: 361
Length adjustment: 31
Effective length of query: 399
Effective length of database: 330
Effective search space:   131670
Effective search space used:   131670
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 N515DRAFT_1430 N515DRAFT_1430 (phosphoserine aminotransferase apoenzyme)
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.25920.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.3e-159  515.5   0.0   3.7e-159  515.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430  N515DRAFT_1430 phosphoserine ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1430  N515DRAFT_1430 phosphoserine aminotransferase apoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.3   0.0  3.7e-159  3.7e-159       2     358 .]       5     360 ..       4     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 515.3 bits;  conditional E-value: 3.7e-159
                                    TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevl 67 
                                                   nFsaGPaa+p++vle+aq+elld+ng+g+svme+sHR k+f  ++e+ae dlreLl+ip +y+vl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430   5 WNFSAGPAAIPTAVLERAQRELLDWNGSGASVMELSHRGKRFIGLAEQAEADLRELLKIPADYAVL 70 
                                                  7***************************************************************** PP

                                    TIGR01364  68 flqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeee 133
                                                  flqGGat+ fa++plnl+ e++ adyiv G+w++ka++ea  +++ v+v+as+++++y ++p + +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430  71 FLQGGATQHFAQIPLNLAGEGDSADYIVNGHWGEKAASEAASYVR-VNVAASSRNEQYLRLPPRAS 135
                                                  *******************************************99.******************** PP

                                    TIGR01364 134 lelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpa 199
                                                  ++l+++aayv+++ neti+Gve++++pev ++plvaD+ss+il++++dvs++gliyaGaqKniGp+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 136 WQLDPRAAYVHYTPNETIHGVEYHDVPEVGEVPLVADMSSNILAEPLDVSRFGLIYAGAQKNIGPS 201
                                                  ****************************************************************** PP

                                    TIGR01364 200 GvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekkn 265
                                                  G++v+i+r+dll+ra + ++++++Y+ +a nds++ntp t+++y++gl+++wlke+GG+++++++n
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 202 GLVVMIIRRDLLQRAARPMAKIFRYAEHAANDSMLNTPNTWGWYLAGLTFQWLKEQGGLEAMAHRN 267
                                                  ****************************************************************** PP

                                    TIGR01364 266 qeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGi 331
                                                  ++Ka llY+aid s g+y+n+++++aRs+mnv+Ftl+++ l++ Flke+e++gl++lkGh+++GG+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 268 RDKAGLLYQAIDGSGGYYRNPIDPAARSRMNVPFTLHDSALDADFLKESEAAGLLALKGHKALGGM 333
                                                  ****************************************************************** PP

                                    TIGR01364 332 RasiYnalpleevqaLvdfmkeFekkh 358
                                                  Ras+Yna+ple+vq Lv+fm++F+++h
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1430 334 RASLYNAVPLEAVQVLVQFMRDFAARH 360
                                                  ***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (361 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.89
//
[ok]

This GapMind analysis is from Apr 09 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