Alignments for a candidate for trpD_2 in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Caulobacter crescentus NA1000

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate CCNA_01975 CCNA_01975 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__Caulo:CCNA_01975
          Length = 341

 Score =  273 bits (699), Expect = 3e-78
 Identities = 160/321 (49%), Positives = 203/321 (63%), Gaps = 7/321 (2%)

Query: 10  GEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRVH 69
           G+ L++ +A     A + GE +P + A  + A+ LRGE   EIAA ARAMR AA PL  H
Sbjct: 15  GQTLDDSDAELFFAACLRGEPTPAQVAAAVTAIRLRGETVGEIAACARAMRRAAIPLE-H 73

Query: 70  RRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGVDL 129
              ++D+ GTGGDG   +N+ST    VAA GG+ VAKHGNRA +S++G+AD+L ALGV++
Sbjct: 74  PYDVIDVCGTGGDGLHTLNISTAVGFVAAGGGLKVAKHGNRAITSKSGTADVLTALGVNI 133

Query: 130 EAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADAYV 189
           +A  E+  +A++E G  FLFA+  H AM+HV+P+R +LG RT+FNLLGPLTNPAGA   V
Sbjct: 134 DATREQQRKALDEAGICFLFAQAHHGAMKHVSPIRQQLGFRTIFNLLGPLTNPAGAKRQV 193

Query: 190 LGVFSPEWLAPMAEALERLGA-RGLVVHGEGADEL-VLGENRVVEVGKGA---YALTPEE 244
           +GV +P ++ P+A+AL  LGA R   VHG G DEL   GE  V E   G    + +TPE 
Sbjct: 194 VGVSAPRFVEPIAKALGALGAERAWSVHGSGMDELTTTGETEVAEWRDGVVRLFKITPEA 253

Query: 245 VGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKEGV 304
           VGL RA L  L GG P  NAA   RL  G E GP  D V L A A F  A K  +L EGV
Sbjct: 254 VGLPRAALADLTGGDPAFNAAALTRLFDG-ETGPYRDIVLLNAAAAFLVADKVETLVEGV 312

Query: 305 ALAREVLASGEAYLLLERYVA 325
           ALA E + SG A   L   VA
Sbjct: 313 ALAAEAIDSGRAKAALAGLVA 333


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: 283
Number of extensions: 12
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: 341
Length adjustment: 28
Effective length of query: 301
Effective length of database: 313
Effective search space:    94213
Effective search space used:    94213
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 CCNA_01975 CCNA_01975 (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.30848.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.6e-118  379.5   0.2   8.7e-118  379.3   0.2    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01975  CCNA_01975 anthranilate phosphor


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01975  CCNA_01975 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.3   0.2  8.7e-118  8.7e-118       2     328 ..      10     332 ..       9     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.3 bits;  conditional E-value: 8.7e-118
                             TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 
                                            kl+d+++L++ +ae ++ + ++ge ++aq+aA+++a+r +get+ eia+ a+a+r+ a  +e+   ++++D+
  lcl|FitnessBrowser__Caulo:CCNA_01975  10 AKLADGQTLDDSDAELFFAACLRGEPTPAQVAAAVTAIRLRGETVGEIAACARAMRRAAIPLEH--PYDVIDV 80 
                                           799***********************************************************87..7****** PP

                             TIGR01245  75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlf 147
                                           +GTGGDgl+t+NiSTa  +vaa+ G+kvaKhGnr+++sksG aDvL algvn++++ e+ +++l+e gi+Flf
  lcl|FitnessBrowser__Caulo:CCNA_01975  81 CGTGGDGLHTLNISTAVGFVAAGGGLKVAKHGNRAITSKSGTADVLTALGVNIDATREQQRKALDEAGICFLF 153
                                           ************************************************************************* PP

                             TIGR01245 148 APkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220
                                           A ++h a+k+v p+R++Lg+rt+fNlLGPL+nPa ak+qv+Gv+ + +ve +a++l +lg++ra  vhg +g+
  lcl|FitnessBrowser__Caulo:CCNA_01975 154 AQAHHGAMKHVSPIRQQLGFRTIFNLLGPLTNPAGAKRQVVGVSAPRFVEPIAKALGALGAERAWSVHG-SGM 225
                                           *********************************************************************.*** PP

                             TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaa 293
                                           DE+++tget+vae +dg ++ ++++pe  gl+ra l +l gg+++ na++l++++ g+  ++ rdiv+lNaaa
  lcl|FitnessBrowser__Caulo:CCNA_01975 226 DELTTTGETEVAEWRDGVVRLFKITPEAVGLPRAALADLTGGDPAFNAAALTRLFDGET-GPYRDIVLLNAAA 297
                                           ****************************************************9999998.9************ PP

                             TIGR01245 294 alyvagkakdlkegvelakeaiksgkalekleelv 328
                                           a +va+k+++l egv la eai+sg+a + l+ lv
  lcl|FitnessBrowser__Caulo:CCNA_01975 298 AFLVADKVETLVEGVALAAEAIDSGRAKAALAGLV 332
                                           ****************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (341 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 12.41
//
[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