GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC 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.7850.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.34
//
[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:

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:

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:

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:

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