Alignments for a candidate for trpD_2 in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Sphingomonas koreensis DSMZ 15582

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate Ga0059261_0929 Ga0059261_0929 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__Korea:Ga0059261_0929
          Length = 331

 Score =  233 bits (594), Expect = 5e-66
 Identities = 139/318 (43%), Positives = 185/318 (58%), Gaps = 7/318 (2%)

Query: 13  LEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRVHRRP 72
           L  E A +    ++ G          L+ALS RGE   EIA  ARAMR+   P+      
Sbjct: 14  LAREAAAQAFADILDGSAPEPEIEAFLIALSERGETSIEIAEAARAMRQRVIPVSAPANA 73

Query: 73  LLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGVDLEAP 132
           + D+ GTGGDG   +N+ST  A+V AA GV VAKHGNRAASS++G+AD LEALG+DL+  
Sbjct: 74  I-DVCGTGGDGHHTLNVSTAVAIVVAAAGVPVAKHGNRAASSKSGAADTLEALGLDLDRA 132

Query: 133 PERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADAYVLGV 192
                  + +LG  FLFA   HPAM  +AP+R  +  RT+FNL+GPL NPAG    ++G+
Sbjct: 133 AANAEAHLNDLGIAFLFAAKHHPAMGRIAPLRRRIARRTIFNLMGPLANPAGVQRQLIGI 192

Query: 193 FSPEWLAPMAEALERLGARG--LVVHGEGADEL-VLGENRVVEVGKGA--YALTPEEVGL 247
             P++    AEALE+LG +G  +V   EG DEL   G + VV +G  +    +TP + GL
Sbjct: 193 ARPDYAPIYAEALEQLGVKGAAIVAGEEGLDELSPEGGSLVVSIGDVSLPVRVTPADAGL 252

Query: 248 KRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKEGVALA 307
              PL +L+GG   ENAA  RRLL G E+GP  DAV   + A    AG+   L+EG   A
Sbjct: 253 PSHPLVSLRGGDARENAAALRRLLLG-ERGPYRDAVLFNSAAALVVAGEAVDLREGAEEA 311

Query: 308 REVLASGEAYLLLERYVA 325
            E +  G A  LL+ ++A
Sbjct: 312 AETIDKGLANALLDCWIA 329


Lambda     K      H
   0.317    0.136    0.380 

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: 331
Number of extensions: 14
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: 329
Length of database: 331
Length adjustment: 28
Effective length of query: 301
Effective length of database: 303
Effective search space:    91203
Effective search space used:    91203
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Ga0059261_0929 Ga0059261_0929 (anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# 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/TIGR01245.hmm
# target sequence database:        /tmp/gapView.3718.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-107  344.2   0.1     5e-107  344.0   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0929  Ga0059261_0929 anthranilate phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0929  Ga0059261_0929 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.0   0.1    5e-107    5e-107       9     328 ..      13     328 ..      10     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 344.0 bits;  conditional E-value: 5e-107
                                 TIGR01245   9 dLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGT 77 
                                                L++e a+q++  i++g+a + +i A+l+al  +get  eia++a+a+r++   v++   ++++D++GT
  lcl|FitnessBrowser__Korea:Ga0059261_0929  13 PLAREAAAQAFADILDGSAPEPEIEAFLIALSERGETSIEIAEAARAMRQRVIPVSA--PANAIDVCGT 79 
                                               7999***************************************************88..79******** PP

                                 TIGR01245  78 GGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFl 146
                                               GGDg +t+N+STa a+v+aaaGv+vaKhGnr++ssksG+aD+Lealg+ l+  ++++++ l+++gi+Fl
  lcl|FitnessBrowser__Korea:Ga0059261_0929  80 GGDGHHTLNVSTAVAIVVAAAGVPVAKHGNRAASSKSGAADTLEALGLDLDRAAANAEAHLNDLGIAFL 148
                                               ********************************************************************* PP

                                 TIGR01245 147 fAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvh 215
                                               fA k+hpa+ ++ap+R++++ rt+fNl+GPL+nPa +++q++G++++d++ ++ae+l++lgvk a +v 
  lcl|FitnessBrowser__Korea:Ga0059261_0929 149 FAAKHHPAMGRIAPLRRRIARRTIFNLMGPLANPAGVQRQLIGIARPDYAPIYAEALEQLGVKGAAIVA 217
                                               ********************************************************************* PP

                                 TIGR01245 216 gedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakr 284
                                               ge+glDE+s+ g + v+++  +     +++p+d gl+ ++l +l+gg+a+ena++l+++l g+  ++ r
  lcl|FitnessBrowser__Korea:Ga0059261_0929 218 GEEGLDELSPEGGSLVVSIG-DVSLPVRVTPADAGLPSHPLVSLRGGDARENAAALRRLLLGER-GPYR 284
                                               ******************98.5556899**********************************98.99** PP

                                 TIGR01245 285 divvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                               d+v++N aaal+vag+a dl+eg+e a e+i++g a ++l+ ++
  lcl|FitnessBrowser__Korea:Ga0059261_0929 285 DAVLFNSAAALVVAGEAVDLREGAEEAAETIDKGLANALLDCWI 328
                                               ************************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (331 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: 8.06
//
[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