Alignments for a candidate for dapC in Herbaspirillum seropedicae SmR1

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.17357.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.81
//
[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