Alignments for a candidate for metA in Phaeobacter inhibens BS107

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.25561.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.45
//
[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