GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metA in Phaeobacter inhibens BS107

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate GFF1439 PGA1_c14560 homoserine O-succinyltransferase MetA

Query= SwissProt::G4RES5
         (306 letters)



>FitnessBrowser__Phaeo:GFF1439
          Length = 305

 Score =  353 bits (906), Expect = e-102
 Identities = 153/304 (50%), Positives = 223/304 (73%), Gaps = 2/304 (0%)

Query: 1   MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60
           MPI+IP  LPA   L  EGV+VM   ++ARQDIRPL+ GLLNLMP K +TE QFARLI +
Sbjct: 1   MPIKIPSDLPAYDVLTNEGVMVMSPDQAARQDIRPLRIGLLNLMPKKIQTENQFARLIGA 60

Query: 61  TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120
           TPLQIDL+L+R+ +  +++T  +++  FY  +++++ ++FDG ++TGAPI ++ FEDV Y
Sbjct: 61  TPLQIDLSLIRMTEHQTRNTAAEHMAEFYRPFQEIKDQRFDGLIITGAPIEHLEFEDVTY 120

Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180
           W E+ E+ DWTQTNVH T  +CWG  A +++ HGVK++ ++HK FG +RH+ LD   P+L
Sbjct: 121 WDELCEVFDWTQTNVHSTFGVCWGGMAMINYFHGVKKHLLDHKVFGCFRHQNLDPASPYL 180

Query: 181 RGFSDDLAVPVSRYNDIDRQSLS--PDLDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238
           RGFSDD  +PVSR+ +I +  +   P L  L+ S + G C+++D  +RA Y+ NH EYD+
Sbjct: 181 RGFSDDCVIPVSRWTEIRQSEIDARPGLRSLLGSQDAGPCLIEDPSHRALYIFNHFEYDS 240

Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298
            +L  EY RD+ +G    +P+N +P +DPSR P+NRWRSHAHLL+ NWIN+IYQ+TP+++
Sbjct: 241 DTLKQEYDRDVASGTPINVPMNYYPDDDPSRKPQNRWRSHAHLLYGNWINDIYQSTPFDM 300

Query: 299 EKVG 302
            ++G
Sbjct: 301 AEIG 304


Lambda     K      H
   0.321    0.137    0.431 

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: 362
Number of extensions: 15
Number of successful extensions: 2
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: 306
Length of database: 305
Length adjustment: 27
Effective length of query: 279
Effective length of database: 278
Effective search space:    77562
Effective search space used:    77562
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate GFF1439 PGA1_c14560 (homoserine O-succinyltransferase MetA)
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))

# 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/TIGR01001.hmm
# target sequence database:        /tmp/gapView.9527.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01001  [M=301]
Accession:   TIGR01001
Description: metA: homoserine O-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.5e-114  366.5   0.0   7.3e-114  366.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1439  PGA1_c14560 homoserine O-succiny


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1439  PGA1_c14560 homoserine O-succinyltransferase MetA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.3   0.0  7.3e-114  7.3e-114       1     300 [.       1     300 [.       1     301 [. 0.99

  Alignments for each domain:
  == domain 1  score: 366.3 bits;  conditional E-value: 7.3e-114
                          TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsrk 76 
                                        mpi++p++lpa+++l +e+++vm+  +a  qdirpl++ +lnlmpkki+tenq+ rl++ +plq+d+ l+r+++++
  lcl|FitnessBrowser__Phaeo:GFF1439   1 MPIKIPSDLPAYDVLTNEGVMVMSPDQAARQDIRPLRIGLLNLMPKKIQTENQFARLIGATPLQIDLSLIRMTEHQ 76 
                                        9*************************************************************************** PP

                          TIGR01001  77 skntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalkll 152
                                        ++nt +eh+ +fy+ ++e+kd++fdGli+tGap+e lefedv yw+el e+++w+++nv st+ +cw+ +a ++++
  lcl|FitnessBrowser__Phaeo:GFF1439  77 TRNTAAEHMAEFYRPFQEIKDQRFDGLIITGAPIEHLEFEDVTYWDELCEVFDWTQTNVHSTFGVCWGGMAMINYF 152
                                        **************************************************************************** PP

                          TIGR01001 153 ygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaaskder 227
                                        +g++k+ l++k++G ++h+ + + ++ lrgf d  ++p sr++++ + +i++ + l  l+ s++ag  l+   ++r
  lcl|FitnessBrowser__Phaeo:GFF1439 153 HGVKKHLLDHKVFGCFRHQNLdPASPYLRGFSDDCVIPVSRWTEIRQSEIDARPGLRSLLGSQDAGPCLIEDPSHR 228
                                        *******************99899**************************************************** PP

                          TIGR01001 228 nifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpydl 300
                                         +++  h eyd +tl+qey rdv +g  +++p+nyyp+ddp+++p   wrsha+ll+ nw+n ++yq+tp+d+
  lcl|FitnessBrowser__Phaeo:GFF1439 229 ALYIFNHFEYDSDTLKQEYDRDVASGTPINVPMNYYPDDDPSRKPQNRWRSHAHLLYGNWIN-DIYQSTPFDM 300
                                        *************************************************************9.8*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (305 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: 6.44
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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