GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Sulfurihydrogenibium azorense Az-Fu1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_012674011.1 SULAZ_RS00880 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_000021545.1:WP_012674011.1
          Length = 336

 Score =  290 bits (743), Expect = 3e-83
 Identities = 156/328 (47%), Positives = 220/328 (67%), Gaps = 1/328 (0%)

Query: 6   QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65
           ++ +++  E + +  +E++ L ++IM  +++DA + A+L GL++K ET+ EI+ AATVMR
Sbjct: 3   KELIKKITEKKNLSKEEVLFLFQEIMDRKLTDAQLGAVLIGLKMKGETVNEISAAATVMR 62

Query: 66  EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125
           + + +V V D+  +VD  GTGGD   TFN+ST + FV AA GAKVAKHGNRSVSSK GSA
Sbjct: 63  DKAIKVNVKDKSKLVDTCGTGGDNIGTFNVSTISAFVVAASGAKVAKHGNRSVSSKCGSA 122

Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185
           D +E+LG  I++ PE+V   + + G+GF++AP+ HPAMK V   RRE+GVRTIFNILGPL
Sbjct: 123 DLMESLGVKIDMPPEKVERCIDEVGLGFLFAPIFHPAMKNVVRQRREIGVRTIFNILGPL 182

Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245
           +NPA +P  LMGV+  DLV   A+VL  LG +RA VV G +G+DE+SL A TLV ++   
Sbjct: 183 SNPADAPYQLMGVYDKDLVEPIAKVLVNLGIKRAFVVHGLEGLDEVSLTAETLVAQVDGE 242

Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVP-GPALDIVALNAGAALYV 304
            +  Y V PEDFG+   +  +LK  D  E++ + L +L      P  D VALN+G AL V
Sbjct: 243 DIKVYTVKPEDFGLKRVSIEDLKGGDIIENKEIALNILTGKDYSPKTDFVALNSGFALKV 302

Query: 305 AGVADSIADGIVRARQVLADGSARACLD 332
           AGV  SI +GI  A++ +    A   L+
Sbjct: 303 AGVVSSIKEGIELAKESIYSKKAYEVLE 330


Lambda     K      H
   0.320    0.134    0.377 

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: 274
Number of extensions: 9
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: 345
Length of database: 336
Length adjustment: 28
Effective length of query: 317
Effective length of database: 308
Effective search space:    97636
Effective search space used:    97636
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_012674011.1 SULAZ_RS00880 (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.862644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-139  449.0   1.0   6.2e-139  448.8   1.0    1.0  1  NCBI__GCF_000021545.1:WP_012674011.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021545.1:WP_012674011.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.8   1.0  6.2e-139  6.2e-139       1     328 [.       6     333 ..       6     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 448.8 bits;  conditional E-value: 6.2e-139
                             TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvD 73 
                                           ++k++++k+Ls+ee+  l++eim+ +++daq++A+l+ l++kget++ei+++a+++r+ka kv+++++++lvD
  NCBI__GCF_000021545.1:WP_012674011.1   6 IKKITEKKNLSKEEVLFLFQEIMDRKLTDAQLGAVLIGLKMKGETVNEISAAATVMRDKAIKVNVKDKSKLVD 78 
                                           689********************************************************************** PP

                             TIGR01245  74 ivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFl 146
                                           ++GTGGD++ t+N+ST+sa+v+aa G+kvaKhGnrsvssk+GsaD++e lgv++++ pekv+r+++evg+gFl
  NCBI__GCF_000021545.1:WP_012674011.1  79 TCGTGGDNIGTFNVSTISAFVVAASGAKVAKHGNRSVSSKCGSADLMESLGVKIDMPPEKVERCIDEVGLGFL 151
                                           ************************************************************************* PP

                             TIGR01245 147 fAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedg 219
                                           fAP +hpa+k+v+  R+e+gvrt+fN+LGPL+nPa a++q++Gvy+kdlve +a+vl nlg+kra+vvhg +g
  NCBI__GCF_000021545.1:WP_012674011.1 152 FAPIFHPAMKNVVRQRREIGVRTIFNILGPLSNPADAPYQLMGVYDKDLVEPIAKVLVNLGIKRAFVVHGLEG 224
                                           ************************************************************************* PP

                             TIGR01245 220 lDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaa 292
                                           lDE+slt+et va+++ ++i+ yt++pedfglkr ++e+lkgg+  en e+  ++l+gk  ++k+d+v+lN +
  NCBI__GCF_000021545.1:WP_012674011.1 225 LDEVSLTAETLVAQVDGEDIKVYTVKPEDFGLKRVSIEDLKGGDIIENKEIALNILTGKDYSPKTDFVALNSG 297
                                           ************************************************************************* PP

                             TIGR01245 293 aalyvagkakdlkegvelakeaiksgkalekleelv 328
                                           +al+vag+++++keg+elake+i s+ka+e+le+l 
  NCBI__GCF_000021545.1:WP_012674011.1 298 FALKVAGVVSSIKEGIELAKESIYSKKAYEVLEKLR 333
                                           *********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (336 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: 17.73
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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