Alignments for a candidate for trpD_2 in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Synechococcus elongatus PCC 7942

Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate Synpcc7942_2123 Synpcc7942_2123 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8YXQ9
         (362 letters)



>FitnessBrowser__SynE:Synpcc7942_2123
          Length = 348

 Score =  399 bits (1025), Expect = e-116
 Identities = 210/344 (61%), Positives = 259/344 (75%), Gaps = 10/344 (2%)

Query: 17  LLLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGVSADELTGMAEVLQS 76
           +LLQ+L++ ESL   QA  LM+ WLS  +P  LSGA+L AL  KGVSA EL  MA+VLQ 
Sbjct: 13  VLLQRLLNHESLGAVQARALMEQWLSGTLPEALSGALLAALQSKGVSAQELAAMAQVLQE 72

Query: 77  QSKMGTGENYSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAFVAAAYGVPVAKHGNRS 136
           Q+      +  +         ++DTCGTGGDG+ TFNISTAVAFV AA GV VAKHGNRS
Sbjct: 73  QAVAVEASDRRE--------PLVDTCGTGGDGAETFNISTAVAFVTAAAGVKVAKHGNRS 124

Query: 137 ASSLTGSADVLEALGVNLGASPEKVQAALQEVGITFLFAPGWHPALKAVATLRRTLRIRT 196
           AS   GSADVLEALG+NL A  +++ AA+ EVGITFLFAPGWHPA+KAVA LR+ L +RT
Sbjct: 125 ASGRVGSADVLEALGLNLTAPSDRIHAAVDEVGITFLFAPGWHPAMKAVAPLRKILGVRT 184

Query: 197 VFNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIVLHGRERLDEAGLGDLT 256
           VFNLLGPLVNPLRPTGQV+G++ P LL T++ AL  LG ++AIVLHGRE LDE GL D T
Sbjct: 185 VFNLLGPLVNPLRPTGQVIGVYNPGLLPTISGALAELGVRRAIVLHGREGLDEGGLADCT 244

Query: 257 DLAVLSDGELQLTTINPQEVGVTPAPIGALRGGDVQENAEILKAVLQGKGTQAQQDAVAL 316
           DLA++ +G+L    ++P+++G+T AP  AL+GG V+ENA+ILKAVLQGKGT+AQQDAV L
Sbjct: 245 DLAIVREGQLSQQVVDPRDLGLTQAPTVALKGGSVEENADILKAVLQGKGTRAQQDAVLL 304

Query: 317 NAALALQVAGAVPLLDHAQGVSVAKEILQTGTAWAKLAQLVYFL 360
           NAALAL+V   V  LD  QG+S+A+ +L +G AW KL QL  FL
Sbjct: 305 NAALALEVGEQVDRLD--QGISLARSVLASGAAWQKLTQLAAFL 346


Lambda     K      H
   0.314    0.130    0.364 

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: 319
Number of extensions: 12
Number of successful extensions: 3
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: 362
Length of database: 348
Length adjustment: 29
Effective length of query: 333
Effective length of database: 319
Effective search space:   106227
Effective search space used:   106227
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate Synpcc7942_2123 Synpcc7942_2123 (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.11712.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-123  396.8   0.2   4.7e-123  396.7   0.2    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2123  Synpcc7942_2123 anthranilate pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2123  Synpcc7942_2123 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.7   0.2  4.7e-123  4.7e-123       1     329 [.      15     344 ..      15     345 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.7 bits;  conditional E-value: 4.7e-123
                                 TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke.es 68 
                                               l++ll++++L + +a++lm++++sg + +a  +A+l+al+ kg +++e+a++a++l+e+a+ ve++  +
  lcl|FitnessBrowser__SynE:Synpcc7942_2123  15 LQRLLNHESLGAVQARALMEQWLSGTLPEALSGALLAALQSKGVSAQELAAMAQVLQEQAVAVEASdRR 83 
                                               6899***********************************************************998789 PP

                                 TIGR01245  69 eelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvars 137
                                               e lvD++GTGGDg++t+NiSTa a+v aaaGvkvaKhGnrs+s+++GsaDvLealg+nl +  ++++++
  lcl|FitnessBrowser__SynE:Synpcc7942_2123  84 EPLVDTCGTGGDGAETFNISTAVAFVTAAAGVKVAKHGNRSASGRVGSADVLEALGLNLTAPSDRIHAA 152
                                               99******************************************************************* PP

                                 TIGR01245 138 leevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknl 206
                                               ++evgi+FlfAP +hpa+k+vap+Rk LgvrtvfNlLGPL+nP+r++ qv+Gvy++ l+ +++ +l +l
  lcl|FitnessBrowser__SynE:Synpcc7942_2123 153 VDEVGITFLFAPGWHPAMKAVAPLRKILGVRTVFNLLGPLVNPLRPTGQVIGVYNPGLLPTISGALAEL 221
                                               ********************************************************************* PP

                                 TIGR01245 207 gvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevl 275
                                               gv+ra+v+hg++glDE  l + t+ a +++g+ +++ ++p+d+gl++a+  +lkggs eena++lk+vl
  lcl|FitnessBrowser__SynE:Synpcc7942_2123 222 GVRRAIVLHGREGLDEGGLADCTDLAIVREGQLSQQVVDPRDLGLTQAPTVALKGGSVEENADILKAVL 290
                                               ********************************************************************* PP

                                 TIGR01245 276 egkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                               +gk+++a++d+v+lNaa al v ++++ l +g++la+ ++ sg+a++kl++l+a
  lcl|FitnessBrowser__SynE:Synpcc7942_2123 291 QGKGTRAQQDAVLLNAALALEVGEQVDRLDQGISLARSVLASGAAWQKLTQLAA 344
                                               **************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (348 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: 00:00:00.01
# Mc/sec: 9.42
//
[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