Alignments for a candidate for trpD_2 in Azospirillum lipoferum B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Azospirillum lipoferum B510

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_012974214.1 AZL_RS08470 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>NCBI__GCF_000010725.1:WP_012974214.1
          Length = 344

 Score =  249 bits (637), Expect = 5e-71
 Identities = 157/331 (47%), Positives = 198/331 (59%), Gaps = 13/331 (3%)

Query: 6   KAILGEV-----LEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMR 60
           KAILG+V     L E EA      +M+G  +P +  G L+AL +RGE   EIA  AR MR
Sbjct: 9   KAILGKVATGAALTEAEAGFAFDIIMSGNATPSQMGGFLMALRVRGETVDEIAGAARVMR 68

Query: 61  EAARPLRVHRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSAD 120
             A P+      + D  GTGGDG G  N+ST AALV +  GV VAKHGNRA SS++G+AD
Sbjct: 69  SKAIPVEAPPGTI-DTCGTGGDGVGTYNISTAAALVVSTCGVPVAKHGNRAISSKSGAAD 127

Query: 121 LLEALGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLT 180
           +L +LGV+L+     V +A+ + G  FL A   H AMR+V P R ELG RTVFNLLGPL 
Sbjct: 128 VLGSLGVNLDCDFALVRKALWDAGIAFLMAPRHHLAMRNVGPTRVELGTRTVFNLLGPLA 187

Query: 181 NPAGADAYVLGVFSPEWLAPMAEALERLGARGL-VVHG-EGADEL-VLGENRVVEVGKG- 236
           NPA A   VLGVFS +W+AP+A  L+RLG+    VVHG +G DE+   G   V ++  G 
Sbjct: 188 NPATAGRQVLGVFSKQWVAPLAHVLKRLGSEAAWVVHGSDGLDEITTTGPTTVAQLKNGE 247

Query: 237 --AYALTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAA 294
              + + PE+ GL RA +E LKGG  + NAA    L  G  + P  D V L A A    A
Sbjct: 248 VTVFEVKPEDAGLPRARIEDLKGGDAQVNAAAIHALFDG-VRSPYRDIVLLNAAAALLVA 306

Query: 295 GKTPSLKEGVALAREVLASGEAYLLLERYVA 325
           GK  +LKEGVA+A + + SG A   L R VA
Sbjct: 307 GKAATLKEGVAMAADAIDSGGARDRLRRLVA 337


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: 318
Number of extensions: 17
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: 344
Length adjustment: 28
Effective length of query: 301
Effective length of database: 316
Effective search space:    95116
Effective search space used:    95116
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 WP_012974214.1 AZL_RS08470 (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.29874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-123  398.3   0.2   1.6e-123  398.1   0.2    1.0  1  lcl|NCBI__GCF_000010725.1:WP_012974214.1  AZL_RS08470 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010725.1:WP_012974214.1  AZL_RS08470 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.1   0.2  1.6e-123  1.6e-123       2     329 ..      13     337 ..      12     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 398.1 bits;  conditional E-value: 1.6e-123
                                 TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeesee 70 
                                                k++++  L+e+ea  +++ imsg+a+++q++ +l+alrv+get++eiag+a+++r+ka  ve+     
  lcl|NCBI__GCF_000010725.1:WP_012974214.1  13 GKVATGAALTEAEAGFAFDIIMSGNATPSQMGGFLMALRVRGETVDEIAGAARVMRSKAIPVEA--PPG 79 
                                               5788999*******************************************************88..699 PP

                                 TIGR01245  71 lvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsle 139
                                                +D++GTGGDg+ t+NiSTa+alv++++Gv+vaKhGnr++ssksG+aDvL  lgvnl+ + + v+++l 
  lcl|NCBI__GCF_000010725.1:WP_012974214.1  80 TIDTCGTGGDGVGTYNISTAAALVVSTCGVPVAKHGNRAISSKSGAADVLGSLGVNLDCDFALVRKALW 148
                                               ********************************************************************* PP

                                 TIGR01245 140 evgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgv 208
                                               + gi+Fl+AP++h a+++v p+R eLg+rtvfNlLGPL+nPa+a +qvlGv+sk+ v  la+vlk+lg+
  lcl|NCBI__GCF_000010725.1:WP_012974214.1 149 DAGIAFLMAPRHHLAMRNVGPTRVELGTRTVFNLLGPLANPATAGRQVLGVFSKQWVAPLAHVLKRLGS 217
                                               ********************************************************************* PP

                                 TIGR01245 209 kralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevleg 277
                                               + a vvhg+dglDEi++tg+t+va+lk+ge++ ++++ped gl+ra++e+lkgg+a+ na+++++++ g
  lcl|NCBI__GCF_000010725.1:WP_012974214.1 218 EAAWVVHGSDGLDEITTTGPTTVAQLKNGEVTVFEVKPEDAGLPRARIEDLKGGDAQVNAAAIHALFDG 286
                                               ****************************************************************98888 PP

                                 TIGR01245 278 kekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                  ++ rdiv+lNaaaal+vagka++lkegv +a +ai+sg a + l++lva
  lcl|NCBI__GCF_000010725.1:WP_012974214.1 287 VR-SPYRDIVLLNAAAALLVAGKAATLKEGVAMAADAIDSGGARDRLRRLVA 337
                                               77.899*****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (344 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.18
//
[ok]

This GapMind analysis is from Apr 10 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