Alignments for a candidate for dapC in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Cupriavidus basilensis 4G11

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate RR42_RS04455 RR42_RS04455 MFS transporter

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__Cup4G11:RR42_RS04455
          Length = 386

 Score =  362 bits (929), Expect = e-105
 Identities = 186/365 (50%), Positives = 247/365 (67%), Gaps = 9/365 (2%)

Query: 3   QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLN 62
           +++NFS GPA LP EVL QA  E+  W+G G SVME+SHR +EF  +  EA  + R+LL 
Sbjct: 20  RVYNFSPGPAALPTEVLLQAADEMLSWHGSGVSVMEMSHRSREFESIQAEALANLRELLQ 79

Query: 63  VPSNYKVLFCHGGGRGQFAAVPLNIL----GDKTTADYVDAGYWAASAIKEAKKYCTPNV 118
           VP N+++LF  GG  G+   VPLN++     D+  AD+V  G W+  + +EA++Y   N+
Sbjct: 80  VPKNFRILFLQGGAIGENGIVPLNLMRRVNADRPKADFVVTGTWSVKSEQEARRYGEVNI 139

Query: 119 FDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFG----ADVVVAAD 174
             A  T      +  + +W+LSD+AAY+H C NETI G+   + PD G       VV AD
Sbjct: 140 A-ATSTAQKFARIPDVADWKLSDDAAYVHLCTNETIVGVEFQDVPDIGQHRDGGPVVVAD 198

Query: 175 FSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDN 234
            SS ILSRP+D SR  V Y GAQKNIGPAGLTIVIVREDLLG A+  CPS  ++ ++ ++
Sbjct: 199 VSSHILSRPVDWSRVQVAYGGAQKNIGPAGLTIVIVREDLLGHAHPLCPSAFNWRLVAEH 258

Query: 235 GSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKAN 294
            SM+NTPPT++ Y++GLVFKWLKA GGV  +++ N  K+  LY  +D S FYRN++   +
Sbjct: 259 DSMYNTPPTYSIYIAGLVFKWLKAQGGVGAIEQRNIAKSHALYEFLDQSAFYRNEIDPGS 318

Query: 295 RSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFM 354
           RSRMNVPF LAD + +  FL  + A GL  LKGH+ VGGMRAS+YNAMP+EGV AL ++M
Sbjct: 319 RSRMNVPFFLADESRNDAFLAGARANGLVQLKGHKSVGGMRASLYNAMPIEGVAALIEYM 378

Query: 355 VEFER 359
            EFER
Sbjct: 379 REFER 383


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: 417
Number of extensions: 12
Number of successful extensions: 4
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: 386
Length adjustment: 30
Effective length of query: 332
Effective length of database: 356
Effective search space:   118192
Effective search space used:   118192
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: 50 (23.9 bits)

Align candidate RR42_RS04455 RR42_RS04455 (MFS transporter)
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.6103.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-147  477.3   0.0   1.4e-147  477.2   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS04455  RR42_RS04455 MFS transporter


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS04455  RR42_RS04455 MFS transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.2   0.0  1.4e-147  1.4e-147       1     356 [.      21     383 ..      21     385 .. 0.98

  Alignments for each domain:
  == domain 1  score: 477.2 bits;  conditional E-value: 1.4e-147
                                 TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 
                                               ++nFs+GPaalp+evl +a++e+l ++g+g+svme+sHRs+efe++  ea  +lreLl++p+n+++lfl
  lcl|FitnessBrowser__Cup4G11:RR42_RS04455  21 VYNFSPGPAALPTEVLLQAADEMLSWHGSGVSVMEMSHRSREFESIQAEALANLRELLQVPKNFRILFL 89 
                                               59******************************************************************* PP

                                 TIGR01364  70 qGGattqfaavplnllkekk....vadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeel 134
                                               qGGa ++   vplnl+++ +    +ad++vtG+ws k+ +ea+++++ v+++a++  +k+ +ipd  ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS04455  90 QGGAIGENGIVPLNLMRRVNadrpKADFVVTGTWSVKSEQEARRYGE-VNIAATSTAQKFARIPDVADW 157
                                               ****************955445679********************98.*******99************ PP

                                 TIGR01364 135 elkedaayvylcanetieGvefkelpevkk.....aplvaDlssdilsrkidvskygliyaGaqKniGp 198
                                               +l++daayv+lc+neti Gvef+++p+  +      ++vaD+ss+ilsr++d s+ ++ y+GaqKniGp
  lcl|FitnessBrowser__Cup4G11:RR42_RS04455 158 KLSDDAAYVHLCTNETIVGVEFQDVPDIGQhrdggPVVVADVSSHILSRPVDWSRVQVAYGGAQKNIGP 226
                                               **************************999878888899******************************* PP

                                 TIGR01364 199 aGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqe 267
                                               aG+t+vivr+dll++a+  +ps ++++ +ae+ds+yntppt++iy++glv+kwlk++GGv ++e++n +
  lcl|FitnessBrowser__Cup4G11:RR42_RS04455 227 AGLTIVIVREDLLGHAHPLCPSAFNWRLVAEHDSMYNTPPTYSIYIAGLVFKWLKAQGGVGAIEQRNIA 295
                                               ********************************************************************* PP

                                 TIGR01364 268 KakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiY 336
                                               K++ lYe +d+s  fy+n++++ +Rs+mnv+F l++e  ++ Fl+ a+++glv+lkGh+svGG+Ras+Y
  lcl|FitnessBrowser__Cup4G11:RR42_RS04455 296 KSHALYEFLDQSA-FYRNEIDPGSRSRMNVPFFLADESRNDAFLAGARANGLVQLKGHKSVGGMRASLY 363
                                               **********996.******************************************************* PP

                                 TIGR01364 337 nalpleevqaLvdfmkeFek 356
                                               na+p+e+v aL+++m+eFe+
  lcl|FitnessBrowser__Cup4G11:RR42_RS04455 364 NAMPIEGVAALIEYMREFER 383
                                               ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (386 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: 00:00:00.01
# Mc/sec: 10.03
//
[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