Alignments for a candidate for dapC in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Klebsiella michiganensis M5al

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate BWI76_RS09755 BWI76_RS09755 phosphoserine transaminase

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__Koxy:BWI76_RS09755
          Length = 362

 Score =  646 bits (1667), Expect = 0.0
 Identities = 314/362 (86%), Positives = 335/362 (92%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           MAQ++NFSSGPAMLPAEVLK AQ+EL DWNGLGTSVME+SHRGKEFI+VAEEAE+DFR L
Sbjct: 1   MAQVYNFSSGPAMLPAEVLKLAQKELCDWNGLGTSVMEISHRGKEFIKVAEEAEQDFRSL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           LN+PSNYKVLFCHGGGRGQFA +PLN+LGDKT ADYVDAGYWAASA+KEA KYCTPNV D
Sbjct: 61  LNIPSNYKVLFCHGGGRGQFAGIPLNLLGDKTVADYVDAGYWAASAVKEAHKYCTPNVID 120

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
           AK+TVDGLRAVKPM EWQL+  AAY+HYCPNETIDGIAI+E P FG DVVV AD SSTIL
Sbjct: 121 AKITVDGLRAVKPMSEWQLTPGAAYLHYCPNETIDGIAIEEAPSFGDDVVVTADLSSTIL 180

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           SR IDVSRYGVIYAGAQKNIGPAGLT++IVREDLLGKA++ACPSILDYSIL+ N SMFNT
Sbjct: 181 SREIDVSRYGVIYAGAQKNIGPAGLTLIIVREDLLGKASVACPSILDYSILSANDSMFNT 240

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300
           PPTFAWYLSGLVFKWLK  GGVA MDKINQQKA+LLY  IDNS FYRNDVA ANRSRMNV
Sbjct: 241 PPTFAWYLSGLVFKWLKEQGGVAAMDKINQQKADLLYSTIDNSAFYRNDVAAANRSRMNV 300

Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360
           PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPL GVKALTDFM +FERR
Sbjct: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLAGVKALTDFMQDFERR 360

Query: 361 HG 362
           HG
Sbjct: 361 HG 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: 510
Number of extensions: 7
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: 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 BWI76_RS09755 BWI76_RS09755 (phosphoserine 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.11323.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     1e-156  507.2   0.0   1.2e-156  507.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS09755  BWI76_RS09755 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS09755  BWI76_RS09755 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.1   0.0  1.2e-156  1.2e-156       1     358 []       4     361 ..       4     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 507.1 bits;  conditional E-value: 1.2e-156
                               TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqG 71 
                                             ++nFs+GPa+lp evl+ aqkel+d+nglg+svmeisHR kef kv+eeae+d+r+Llnip+ny+vlf+ G
  lcl|FitnessBrowser__Koxy:BWI76_RS09755   4 VYNFSSGPAMLPAEVLKLAQKELCDWNGLGTSVMEISHRGKEFIKVAEEAEQDFRSLLNIPSNYKVLFCHG 74 
                                             59********************************************************************* PP

                               TIGR01364  72 GattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvase.eekkyskipdeeelelkedaa 141
                                             G+++qfa +plnll +k+vady+ +G+w++ a+kea+k+++  +v+  +   +   ++   +e++l++ aa
  lcl|FitnessBrowser__Koxy:BWI76_RS09755  75 GGRGQFAGIPLNLLGDKTVADYVDAGYWAASAVKEAHKYCT-PNVIDAKiTVDGLRAVKPMSEWQLTPGAA 144
                                             *****************************************.4544444478999**************** PP

                               TIGR01364 142 yvylcanetieGvefkelpevkk.aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdll 211
                                             y+++c neti+G+ ++e+p++ + +++ aDlss ilsr+idvs+yg+iyaGaqKniGpaG+t++ivr+dll
  lcl|FitnessBrowser__Koxy:BWI76_RS09755 145 YLHYCPNETIDGIAIEEAPSFGDdVVVTADLSSTILSREIDVSRYGVIYAGAQKNIGPAGLTLIIVREDLL 215
                                             *********************99567779****************************************** PP

                               TIGR01364 212 erakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegf 282
                                             ++a+  +ps+ldY+il+ nds++ntpptfa+y++glv+kwlke+GGv++++k nq+Ka+llY +id+s  f
  lcl|FitnessBrowser__Koxy:BWI76_RS09755 216 GKASVACPSILDYSILSANDSMFNTPPTFAWYLSGLVFKWLKEQGGVAAMDKINQQKADLLYSTIDNSA-F 285
                                             ******************************************************************995.* PP

                               TIGR01364 283 yknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmke 353
                                             y+n+v++++Rs+mnv+F+l+++ l+k Fl+e+ ++gl++lkGhr+vGG+RasiYna+pl++v+aL dfm++
  lcl|FitnessBrowser__Koxy:BWI76_RS09755 286 YRNDVAAANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLAGVKALTDFMQD 356
                                             *********************************************************************** PP

                               TIGR01364 354 Fekkh 358
                                             Fe++h
  lcl|FitnessBrowser__Koxy:BWI76_RS09755 357 FERRH 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.85
//
[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