GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Herbaspirillum seropedicae SmR1

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate HSERO_RS18435 HSERO_RS18435 MFS transporter

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__HerbieS:HSERO_RS18435
          Length = 370

 Score =  399 bits (1025), Expect = e-116
 Identities = 205/371 (55%), Positives = 263/371 (70%), Gaps = 14/371 (3%)

Query: 4   IFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNV 63
           ++NFS+GPA+LP EVL+QA  E+ DW+G G SVME+SHRGKE++ + E A  D R L+N+
Sbjct: 2   VYNFSAGPAVLPKEVLQQAADEMLDWHGSGMSVMEMSHRGKEYMSIIEAALADVRALMNI 61

Query: 64  PSNYKVLFCHGGGRGQFAAVPLNILGDKT--------TADYVDAGYWAASAIKEAKKYCT 115
           PSNYKVLF  GG   + A +P+N+   ++         ADY++ G W+  +IKEA +YCT
Sbjct: 62  PSNYKVLFLQGGAIAENAIIPMNLAALRSPAGKHEVGVADYINTGSWSTKSIKEAGRYCT 121

Query: 116 PNVFDAKVTVDGLRAVKPMR-EWQLSDNAAYMHYCPNETIDGIAIDETPDFGADV---VV 171
            NV  A  + D   A  P R +W+LS NAAY+H C NETIDG+    TP+  AD     +
Sbjct: 122 VNV--AASSADRKFASIPARADWKLSRNAAYVHICSNETIDGVEYQYTPEVAADTDGAPL 179

Query: 172 AADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSIL 231
            AD SS ILSR +DVS+YGVIY GAQKNIGPAG+TIVIVREDLLG A   CPS  D+ I+
Sbjct: 180 VADMSSHILSREVDVSKYGVIYGGAQKNIGPAGVTIVIVREDLLGHALPFCPSAFDWKIV 239

Query: 232 NDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVA 291
            DN SM+NTPPT+A Y++GLVF+W+K  GGVA ++  N  KA LLYG +D++DFY N +A
Sbjct: 240 ADNDSMYNTPPTYAIYIAGLVFQWIKRQGGVAALEARNIAKARLLYGYLDSTDFYSNRIA 299

Query: 292 KANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALT 351
              RSRMNVPF L D AL+  FL  +   GL  LKGH+ VGGMRASIYNAMP+EGV+AL 
Sbjct: 300 ADCRSRMNVPFFLRDDALNDTFLAGAKERGLLQLKGHKSVGGMRASIYNAMPIEGVQALV 359

Query: 352 DFMVEFERRHG 362
           D++ +FE++HG
Sbjct: 360 DYLKDFEKQHG 370


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: 430
Number of extensions: 20
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: 370
Length adjustment: 30
Effective length of query: 332
Effective length of database: 340
Effective search space:   112880
Effective search space used:   112880
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 HSERO_RS18435 HSERO_RS18435 (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.10103.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.7e-161  520.8   0.0   8.7e-161  520.7   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS18435  HSERO_RS18435 MFS transporter


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS18435  HSERO_RS18435 MFS transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.7   0.0  8.7e-161  8.7e-161       1     358 []       2     369 ..       2     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 520.7 bits;  conditional E-value: 8.7e-161
                                  TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlf 68 
                                                ++nFsaGPa+lp+evl++a++e+ld++g+g+svme+sHR ke+++++e a  d+r L+nip+ny+vlf
  lcl|FitnessBrowser__HerbieS:HSERO_RS18435   2 VYNFSAGPAVLPKEVLQQAADEMLDWHGSGMSVMEMSHRGKEYMSIIEAALADVRALMNIPSNYKVLF 69 
                                                59****************************************************************** PP

                                  TIGR01364  69 lqGGattqfaavplnllkekk........vadyivtGawskkalkeakkltkevkvvaseeekkyski 128
                                                lqGGa  + a +p+nl++ ++        vadyi+tG+ws+k++kea ++++ v+v+as++++k+ +i
  lcl|FitnessBrowser__HerbieS:HSERO_RS18435  70 LQGGAIAENAIIPMNLAALRSpagkhevgVADYINTGSWSTKSIKEAGRYCT-VNVAASSADRKFASI 136
                                                *****************944445557788**********************9.*************** PP

                                  TIGR01364 129 pdeeelelkedaayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvskygliyaGa 192
                                                p + +++l+ +aayv++c+neti+Gve++ +pev+     aplvaD+ss+ilsr++dvskyg+iy+Ga
  lcl|FitnessBrowser__HerbieS:HSERO_RS18435 137 PARADWKLSRNAAYVHICSNETIDGVEYQYTPEVAAdtdgAPLVADMSSHILSREVDVSKYGVIYGGA 204
                                                ********************************998888899*************************** PP

                                  TIGR01364 193 qKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkk 260
                                                qKniGpaGvt+vivr+dll++a   +ps +d+ki+a+nds+yntppt+aiy++glv++w+k++GGv++
  lcl|FitnessBrowser__HerbieS:HSERO_RS18435 205 QKNIGPAGVTIVIVREDLLGHALPFCPSAFDWKIVADNDSMYNTPPTYAIYIAGLVFQWIKRQGGVAA 272
                                                ******************************************************************** PP

                                  TIGR01364 261 lekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsv 328
                                                le++n +Ka+llY ++d++ +fy n++++++Rs+mnv+F l+++ l+++Fl+ a+e+gl++lkGh+sv
  lcl|FitnessBrowser__HerbieS:HSERO_RS18435 273 LEARNIAKARLLYGYLDST-DFYSNRIAADCRSRMNVPFFLRDDALNDTFLAGAKERGLLQLKGHKSV 339
                                                *****************77.6*********************************************** PP

                                  TIGR01364 329 GGiRasiYnalpleevqaLvdfmkeFekkh 358
                                                GG+RasiYna+p+e+vqaLvd++k+Fek+h
  lcl|FitnessBrowser__HerbieS:HSERO_RS18435 340 GGMRASIYNAMPIEGVQALVDYLKDFEKQH 369
                                                ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (370 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: 7.73
//
[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