Alignments for a candidate for trpD_2 in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Halorhodospira halophila SL1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_011814866.1 HHAL_RS10510 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_000015585.1:WP_011814866.1
          Length = 342

 Score =  301 bits (770), Expect = 2e-86
 Identities = 156/334 (46%), Positives = 219/334 (65%), Gaps = 1/334 (0%)

Query: 8   ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67
           AL+R  E++++  DEM  + R IM G  + A +   L G+R+K ET+ E+A AA+VMRE 
Sbjct: 6   ALRRITENQDLSPDEMTAVFRTIMTGGATPAQIGGFLIGMRLKGETVQEMAAAASVMREL 65

Query: 68  SRRVEVTDRRH-MVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSAD 126
           + RV+V D  H +VD  GTGGD   T N+ST A FV AAGG  VAKHGNRSVS +SGSAD
Sbjct: 66  AERVDVGDDFHRLVDTCGTGGDARGTLNVSTAAAFVTAAGGIPVAKHGNRSVSGRSGSAD 125

Query: 127 ALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLT 186
            LEA GA +EL  E VA  + +  +GF++AP+HH AMK     R+E+GVRT+FN++GPL+
Sbjct: 126 LLEACGATLELSSEAVAECIRRVNVGFLFAPLHHSAMKHAVGPRKELGVRTLFNLVGPLS 185

Query: 187 NPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQ 246
           NPAG+   L+GVF  + V   A VLQ LG++  LVV   DG+DE+S+ A T + ELR+GQ
Sbjct: 186 NPAGARRQLLGVFGQEWVRPVAEVLQALGSDHVLVVHAEDGLDEISIAAPTRIAELRNGQ 245

Query: 247 VHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYVAG 306
           + EY V PED G+  +    + ++   +S AM+          A++++A NAGAALYV G
Sbjct: 246 IEEYTVTPEDLGLRSAPLNEVTISGTKDSLAMIRAAFSGERIAAMELIAANAGAALYVGG 305

Query: 307 VADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
            A  +  G+ RAR+++  G+A   L+ +VA T++
Sbjct: 306 EAPDLRRGVERARELMTSGAAAQTLERFVATTKE 339


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: 305
Number of extensions: 12
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: 342
Length adjustment: 29
Effective length of query: 316
Effective length of database: 313
Effective search space:    98908
Effective search space used:    98908
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_011814866.1 HHAL_RS10510 (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.49613.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-125  402.9   0.3   6.6e-125  402.7   0.3    1.0  1  NCBI__GCF_000015585.1:WP_011814866.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_011814866.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.7   0.3  6.6e-125  6.6e-125       1     329 [.       7     335 ..       7     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 402.7 bits;  conditional E-value: 6.6e-125
                             TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke.eseelv 72 
                                           l+++++n+dLs +e+++++++im+g a++aqi+ +l+ +r kget++e+a++a ++re a++v++  + ++lv
  NCBI__GCF_000015585.1:WP_011814866.1   7 LRRITENQDLSPDEMTAVFRTIMTGGATPAQIGGFLIGMRLKGETVQEMAAAASVMRELAERVDVGdDFHRLV 79 
                                           5799************************************************************986889*** PP

                             TIGR01245  73 DivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigF 145
                                           D++GTGGD+  t+N+STa+a+v aa G++vaKhGnrsvs++sGsaD+Lea g++lels e+va+++++v++gF
  NCBI__GCF_000015585.1:WP_011814866.1  80 DTCGTGGDARGTLNVSTAAAFVTAAGGIPVAKHGNRSVSGRSGSADLLEACGATLELSSEAVAECIRRVNVGF 152
                                           ************************************************************************* PP

                             TIGR01245 146 lfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhged 218
                                           lfAP +h+a+k++++ RkeLgvrt+fNl+GPL+nPa a++q+lGv+ ++ v+ +aevl++lg++++lvvh+ed
  NCBI__GCF_000015585.1:WP_011814866.1 153 LFAPLHHSAMKHAVGPRKELGVRTLFNLVGPLSNPAGARRQLLGVFGQEWVRPVAEVLQALGSDHVLVVHAED 225
                                           ************************************************************************* PP

                             TIGR01245 219 glDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNa 291
                                           glDEis+ ++t++ael++g+ieeyt++ped+gl  a+l+e+ ++ +++++++++++++g+   a+ +++++Na
  NCBI__GCF_000015585.1:WP_011814866.1 226 GLDEISIAAPTRIAELRNGQIEEYTVTPEDLGLRSAPLNEVTISGTKDSLAMIRAAFSGER-IAAMELIAANA 297
                                           ***********************************************************99.7779******* PP

                             TIGR01245 292 aaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                           +aalyv g+a dl+ gve+a+e ++sg+a+++le++va
  NCBI__GCF_000015585.1:WP_011814866.1 298 GAALYVGGEAPDLRRGVERARELMTSGAAAQTLERFVA 335
                                           **********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (342 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: 17.68
//
[ok]

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