Alignments for a candidate for trpD_2 in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Chlorobaculum tepidum TLS

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate NP_662492.1 CT1609 anthranilate phosphoribosyltransferase

Query= curated2:B3QM44
         (351 letters)



>NCBI__GCF_000006985.1:NP_662492.1
          Length = 351

 Score =  527 bits (1357), Expect = e-154
 Identities = 258/346 (74%), Positives = 299/346 (86%)

Query: 1   MRQQELIQKLLAGADLSAQEMEACIDSIMENRFTDAGTGAILALLQKKGVTPTEAIGAYE 60
           MRQQE++QKLL G DLS QEME C++SIMENRFTDAGTGAILALLQKKG TP E IGA  
Sbjct: 1   MRQQEILQKLLEGHDLSRQEMETCMNSIMENRFTDAGTGAILALLQKKGATPAEVIGACA 60

Query: 61  NLMTRVTPITLPAHAVDTCGTGGDHRGTFNISTAAAFIAAGAGVPIAKHGNRSITSKCGS 120
           +++++ TP+TL   AVDTCGTGGDH GTFNISTAAAFIA GAG+PIAKHGNRSITSKCGS
Sbjct: 61  SIVSKSTPVTLDQQAVDTCGTGGDHTGTFNISTAAAFIACGAGIPIAKHGNRSITSKCGS 120

Query: 121 ADVLEALGYRVDLPASATEEQFRETGFAFLFAPLYHPSMKAVASIRRELGIRTLFNLLGP 180
           ADVLEALGY+VDLP  ATEE FRETGFAFLFAPLYHPSMKAVA+IR+ELGI+T+FN+LGP
Sbjct: 121 ADVLEALGYQVDLPPCATEELFRETGFAFLFAPLYHPSMKAVAAIRKELGIKTIFNMLGP 180

Query: 181 LINPAKVKRQFIGVFDPSVMELYADVLIHAGCQHAMIVHGKTEHGDGLDEASVSGPTTII 240
           +INPA V+RQ IGVFDPSVM++YA+VL+  GC+HAM+VHG T +  GLDE SV GPT++I
Sbjct: 181 IINPAGVRRQLIGVFDPSVMDIYAEVLLLNGCEHAMLVHGSTGNSMGLDEPSVCGPTSMI 240

Query: 241 ELFEGRLCHHTVNPEDFGLNRWSIDELAGGDAETNAQIIRQILDGSATQAQIDAALFASA 300
           EL +G++  HTV PEDFGL RW I ELAGGD+  NAQIIR+ILDGSA QA+IDAALFASA
Sbjct: 241 ELHQGQIIRHTVEPEDFGLGRWDIGELAGGDSHVNAQIIREILDGSAPQAKIDAALFASA 300

Query: 301 ITCYVSGMGSCIDEGMSMSKESLESLAAMENMNRIIEVNNRLAEEC 346
           ITCYVSG  SCIDEGMS+SK SLE+  A++ MN II+ N RLA++C
Sbjct: 301 ITCYVSGKASCIDEGMSLSKGSLETCEALDKMNLIIKTNQRLAQKC 346


Lambda     K      H
   0.318    0.134    0.386 

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: 449
Number of extensions: 9
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: 351
Length of database: 351
Length adjustment: 29
Effective length of query: 322
Effective length of database: 322
Effective search space:   103684
Effective search space used:   103684
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate NP_662492.1 CT1609 (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.12117.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.3e-112  362.3   0.0   1.5e-112  362.1   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_662492.1  CT1609 anthranilate phosphoribos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_662492.1  CT1609 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.1   0.0  1.5e-112  1.5e-112       1     328 [.       7     336 ..       7     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 362.1 bits;  conditional E-value: 1.5e-112
                              TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelv 72 
                                            l+kll+++dLs++e+e+ m+ im+++++da  +Ail++l+ kg t+ e+ g+   + +k++ v+ +  +++v
  lcl|NCBI__GCF_000006985.1:NP_662492.1   7 LQKLLEGHDLSRQEMETCMNSIMENRFTDAGTGAILALLQKKGATPAEVIGACASIVSKSTPVTLD--QQAV 76 
                                            689************************************************************995..9*** PP

                              TIGR01245  73 DivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgig 144
                                            D++GTGGD++ t+NiSTa+a++a +aG+++aKhGnrs++sk+GsaDvLealg++++l p + ++ ++e+g++
  lcl|NCBI__GCF_000006985.1:NP_662492.1  77 DTCGTGGDHTGTFNISTAAAFIACGAGIPIAKHGNRSITSKCGSADVLEALGYQVDLPPCATEELFRETGFA 148
                                            ************************************************************************ PP

                              TIGR01245 145 FlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhg 216
                                            FlfAP yhp++k+va++RkeLg++t+fN+LGP++nPa +++q++Gv+++++++++aevl   g ++a++vhg
  lcl|NCBI__GCF_000006985.1:NP_662492.1 149 FLFAPLYHPSMKAVAAIRKELGIKTIFNMLGPIINPAGVRRQLIGVFDPSVMDIYAEVLLLNGCEHAMLVHG 220
                                            ************************************************************************ PP

                              TIGR01245 217 ....edglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakr 284
                                                ++glDE s++g+t ++el++g+i + t++pedfgl r ++ el+gg+ + na++++e+l g + +ak 
  lcl|NCBI__GCF_000006985.1:NP_662492.1 221 stgnSMGLDEPSVCGPTSMIELHQGQIIRHTVEPEDFGLGRWDIGELAGGDSHVNAQIIREILDGSAPQAKI 292
                                            8888899***************************************************************** PP

                              TIGR01245 285 divvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                            d+ ++  a+  yv+gka+ + eg++l k ++++ +al+k++ ++
  lcl|NCBI__GCF_000006985.1:NP_662492.1 293 DAALFASAITCYVSGKASCIDEGMSLSKGSLETCEALDKMNLII 336
                                            ***********************************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (351 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: 11.12
//
[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