Alignments for a candidate for trpD_2 in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Herbaspirillum seropedicae SmR1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate HSERO_RS19445 HSERO_RS19445 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__HerbieS:HSERO_RS19445
          Length = 345

 Score =  470 bits (1210), Expect = e-137
 Identities = 234/340 (68%), Positives = 279/340 (82%)

Query: 1   MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60
           MPITPQ+AL R IEHREIFHDEM+ L RQIM GE+S  M++A+  GLRVKKE+IGEIA A
Sbjct: 1   MPITPQEALLRCIEHREIFHDEMLTLFRQIMSGEMSPVMIAALTMGLRVKKESIGEIAAA 60

Query: 61  ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120
           A VMREF+ +V + D   ++DIVGTGGDG+HTFNIST +MFVAAA GA+VAKHG RSVSS
Sbjct: 61  AQVMREFATKVPMADTSRLLDIVGTGGDGAHTFNISTASMFVAAAAGARVAKHGGRSVSS 120

Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180
            SGSAD LEALGA I LQPEQVA S+AQTGIGFM+AP HH AMK  APVR+E+GVRTIFN
Sbjct: 121 SSGSADVLEALGADINLQPEQVAQSIAQTGIGFMFAPNHHAAMKHAAPVRKELGVRTIFN 180

Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240
           ILGPLTNPAG+PNILMGVFHPDLVGIQ RVLQ LGA+ A+VVWGRD +DE++LG  T+VG
Sbjct: 181 ILGPLTNPAGAPNILMGVFHPDLVGIQVRVLQRLGAQHAIVVWGRDNLDEVTLGGATMVG 240

Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300
           EL +G++ EYE+HPEDFG++M ASRNL+V++AAES+  + + L   PGP  DIV +NA  
Sbjct: 241 ELINGEIREYEIHPEDFGLSMFASRNLQVSNAAESKEKIFEALRGEPGPVHDIVVINAAT 300

Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
           ALY AGVA SIA+G+  AR  +A G+ARA LD +V  T+Q
Sbjct: 301 ALYAAGVAPSIAEGLQTARATIASGAARAKLDQFVQVTRQ 340


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: 393
Number of extensions: 8
Number of successful extensions: 1
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: 345
Length adjustment: 29
Effective length of query: 316
Effective length of database: 316
Effective search space:    99856
Effective search space used:    99856
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 HSERO_RS19445 HSERO_RS19445 (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.31844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     2e-129  417.6   2.2   2.3e-129  417.4   2.2    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19445  HSERO_RS19445 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19445  HSERO_RS19445 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.4   2.2  2.3e-129  2.3e-129       3     329 ..      11     336 ..       9     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 417.4 bits;  conditional E-value: 2.3e-129
                                  TIGR01245   3 klldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeesee 70 
                                                ++++++++ ++e+ +l+++imsge+s++ iaA+ + lrvk e++ eia++a+++re a+kv+  ++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19445  11 RCIEHREIFHDEMLTLFRQIMSGEMSPVMIAALTMGLRVKKESIGEIAAAAQVMREFATKVPMADTSR 78 
                                                78999*************************************************************** PP

                                  TIGR01245  71 lvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138
                                                l+DivGTGGDg++t+NiSTas++vaaaaG++vaKhG rsvss+sGsaDvLealg+ ++l+pe+va+s+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19445  79 LLDIVGTGGDGAHTFNISTASMFVAAAAGARVAKHGGRSVSSSSGSADVLEALGADINLQPEQVAQSI 146
                                                ******************************************************************** PP

                                  TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknl 206
                                                +++gigF+fAP++h a+k++apvRkeLgvrt+fN+LGPL+nPa a++ ++Gv+++dlv + ++vl++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS19445 147 AQTGIGFMFAPNHHAAMKHAAPVRKELGVRTIFNILGPLTNPAGAPNILMGVFHPDLVGIQVRVLQRL 214
                                                ******************************************************************** PP

                                  TIGR01245 207 gvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkev 274
                                                g+++a+vv g+d+lDE++l g t v el +gei+ey+++pedfgl +   ++l++++a+e+ e++ e+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19445 215 GAQHAIVVWGRDNLDEVTLGGATMVGELINGEIREYEIHPEDFGLSMFASRNLQVSNAAESKEKIFEA 282
                                                ******************************************************************** PP

                                  TIGR01245 275 legkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                l+g+  ++ +divv+Naa+aly+ag+a +++eg+++a+++i sg+a +kl+++v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19445 283 LRGEP-GPVHDIVVINAATALYAAGVAPSIAEGLQTARATIASGAARAKLDQFVQ 336
                                                ***99.999******************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (345 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.76
//
[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