Alignments for a candidate for trpD_2 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Echinicola vietnamensis KMM 6221, DSM 17526

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate Echvi_2507 Echvi_2507 anthranilate phosphoribosyltransferase

Query= reanno::Pedo557:CA265_RS05010
         (329 letters)



>FitnessBrowser__Cola:Echvi_2507
          Length = 338

 Score =  410 bits (1055), Expect = e-119
 Identities = 201/327 (61%), Positives = 257/327 (78%)

Query: 1   MKKILNHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAM 60
           MK ILNHL E+++  +EEAK+ L  I+ GA+N SQ+AAF+T Y MR+ITV+EL+GFR+AM
Sbjct: 1   MKDILNHLIEHRTLGKEEAKSTLKKITSGAYNQSQMAAFMTVYMMRSITVEELEGFREAM 60

Query: 61  LDMCVKVNLSGYDLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSS 120
           L+ C+ V +  YD +DLCGTGGDGKDTFNISTLSSFVVAGAG +VAKHGN GVSS CGSS
Sbjct: 61  LEQCIPVEIPEYDAMDLCGTGGDGKDTFNISTLSSFVVAGAGQNVAKHGNNGVSSICGSS 120

Query: 121 NVMEYLGYTFTNNEDTLKRNLDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPM 180
           N++   GY FTN+ + +++NLD AGICFLHAPLF+PAMK V PIRKELGVKTFFNMLGPM
Sbjct: 121 NLLAQFGYNFTNDINVIRKNLDEAGICFLHAPLFHPAMKNVGPIRKELGVKTFFNMLGPM 180

Query: 181 VNPGQPKYQMVGVFSLELARLYAYLYQDTDKSYTIVHALEGYDEVSLTCDVKTFSNKGEQ 240
           VNP  PK Q+VGVFSLELARLY YLYQ++   ++I+H+L+GYDEVSLT D K  SN GE+
Sbjct: 181 VNPSFPKKQLVGVFSLELARLYGYLYQNSRVDFSILHSLDGYDEVSLTGDFKMISNSGER 240

Query: 241 ILTLQDMGFDKVEVNAIKGGDTVESSAKIFMDVLNGKATDVQNNVVLCNSALAIKTIKPQ 300
           +++ + +G  +++  +I+GG T+E+SAKIF D+L G+ T+ Q  VVL NSA A+ T    
Sbjct: 241 LISPESIGLPRLDAKSIEGGKTIEASAKIFQDILKGEGTEAQRAVVLANSAAALVTADQS 300

Query: 301 QSFADCFYEAEESLMSKKALNSFKQLL 327
            SF +   +A ESL S KAL +FK+L+
Sbjct: 301 LSFEEGIVKAAESLDSGKALQTFKKLV 327


Lambda     K      H
   0.319    0.134    0.385 

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: 355
Number of extensions: 6
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: 329
Length of database: 338
Length adjustment: 28
Effective length of query: 301
Effective length of database: 310
Effective search space:    93310
Effective search space used:    93310
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 Echvi_2507 Echvi_2507 (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.30577.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   4.7e-100  321.0   0.1   5.4e-100  320.8   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2507  Echvi_2507 anthranilate phosphor


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2507  Echvi_2507 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.8   0.1  5.4e-100  5.4e-100       1     329 [.       5     328 ..       5     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 320.8 bits;  conditional E-value: 5.4e-100
                            TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 
                                          l++l+++++L +eea++ +k+i sg ++++q+aA++++  +++ t+ee++g+ +a++e+   ve  ++++++D 
  lcl|FitnessBrowser__Cola:Echvi_2507   5 LNHLIEHRTLGKEEAKSTLKKITSGAYNQSQMAAFMTVYMMRSITVEELEGFREAMLEQCIPVEI-PEYDAMDL 77 
                                          5789***********************************************************99.7******* PP

                            TIGR01245  75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfA 148
                                          +GTGGDg +t+NiST s++v+a+aG +vaKhGn  vss +Gs+++L ++g+n+ ++++ +++ l+e gi+Fl+A
  lcl|FitnessBrowser__Cola:Echvi_2507  78 CGTGGDGKDTFNISTLSSFVVAGAGQNVAKHGNNGVSSICGSSNLLAQFGYNFTNDINVIRKNLDEAGICFLHA 151
                                          ************************************************************************** PP

                            TIGR01245 149 PkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDE 222
                                          P +hpa+k+v p+RkeLgv+t fN+LGP++nP  +k q++Gv+s +l++++    +n +v+   ++h+ dg DE
  lcl|FitnessBrowser__Cola:Echvi_2507 152 PLFHPAMKNVGPIRKELGVKTFFNMLGPMVNPSFPKKQLVGVFSLELARLYGYLYQNSRVD-FSILHSLDGYDE 224
                                          ************************************************************9.899********* PP

                            TIGR01245 223 isltgetkvaelkdgeieeytlspedfglkraeleelkggsa.eenaellkevlegkekkakrdivvlNaaaal 295
                                          +sltg+ k+++ +     e  +spe++gl+r + ++++gg++ e++a++++++l+g++++a+r++v++N aaal
  lcl|FitnessBrowser__Cola:Echvi_2507 225 VSLTGDFKMISNS----GERLISPESIGLPRLDAKSIEGGKTiEASAKIFQDILKGEGTEAQRAVVLANSAAAL 294
                                          *******999877....46679*****************999899***************************** PP

                            TIGR01245 296 yvagkakdlkegvelakeaiksgkalekleelva 329
                                          ++a++  +++eg+  a e+++sgkal+++++lv+
  lcl|FitnessBrowser__Cola:Echvi_2507 295 VTADQSLSFEEGIVKAAESLDSGKALQTFKKLVN 328
                                          ******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (338 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: 10.42
//
[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