Alignments for a candidate for aroG in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Halomonas desiderata SP1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_086509326.1 BZY95_RS07485 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P00888
         (356 letters)



>NCBI__GCF_002151265.1:WP_086509326.1
          Length = 369

 Score =  338 bits (867), Expect = 1e-97
 Identities = 172/330 (52%), Positives = 221/330 (66%), Gaps = 3/330 (0%)

Query: 14  EQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEY 73
           E  L TP +L+   PL+     ++A  R++I DI+ G D R+LVV GPCSIHDP  ALEY
Sbjct: 36  EMTLPTPGELRRRLPLAPPVTERLAAQRRAIRDIVTGCDDRMLVVVGPCSIHDPLAALEY 95

Query: 74  ARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLE 133
           ARR   LA  +SD L  VMRVY EKPRTTVGWKGL  DP +DGS D+  GL ++R ++ E
Sbjct: 96  ARRLAELAPRISDRLLPVMRVYVEKPRTTVGWKGLAYDPDLDGSGDMARGLHLSRHMMHE 155

Query: 134 LVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGS 193
           +  +GLP+ATE L P    Y  DL +W AIGARTTESQ HRE+ASGL   VGFKN T G 
Sbjct: 156 IAALGLPVATEVLQPMLASYFDDLLAWVAIGARTTESQLHRELASGLEAAVGFKNATSGD 215

Query: 194 LATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPADVAQCEK 252
           +  A++A+RAAA PH+  G+++ G+ AL +T GN   HV+LRGG   PN+    VA+  +
Sbjct: 216 VGVAVDAIRAAAHPHQHFGLDEQGRPALRETTGNSYAHVVLRGGHHGPNHDSRSVAEARR 275

Query: 253 EMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQS 312
            +EQAGL   LMVDCSH N+ KD+RRQ  V   VV Q   G  +++GLM+ES++ EG Q 
Sbjct: 276 ALEQAGLPARLMVDCSHANARKDHRRQGEVLRDVVTQRVQGETALMGLMLESHLEEGRQ- 334

Query: 313 SEQPRSEMKYGVSVTDACISWEMTDALLRE 342
            E     ++YGVSVTD C+ W+ T+ALL E
Sbjct: 335 -ELAPGALRYGVSVTDPCLGWQATEALLLE 363


Lambda     K      H
   0.316    0.131    0.378 

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: 381
Number of extensions: 10
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: 356
Length of database: 369
Length adjustment: 29
Effective length of query: 327
Effective length of database: 340
Effective search space:   111180
Effective search space used:   111180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_086509326.1 BZY95_RS07485 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.4044.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-135  437.5   0.0   1.6e-135  437.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509326.1  BZY95_RS07485 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509326.1  BZY95_RS07485 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.2   0.0  1.6e-135  1.6e-135      10     337 ..      38     367 ..      30     369 .] 0.98

  Alignments for each domain:
  == domain 1  score: 437.2 bits;  conditional E-value: 1.6e-135
                                 TIGR00034  10 elltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaekl 78 
                                                l tP el+++ pl++ ++e++a +r++i di++G ddr+lvv+GPcsihdp aaleya+rl++la ++
  lcl|NCBI__GCF_002151265.1:WP_086509326.1  38 TLPTPGELRRRLPLAPPVTERLAAQRRAIRDIVTGCDDRMLVVVGPCSIHDPLAALEYARRLAELAPRI 106
                                               4679***************************************************************** PP

                                 TIGR00034  79 kddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqy 147
                                               +d+l  vmrvy+ekPrttvGWkGl  dPdl++s d+ +Gl+++r+++ +++ lglp+ate+l+++ + y
  lcl|NCBI__GCF_002151265.1:WP_086509326.1 107 SDRLLPVMRVYVEKPRTTVGWKGLAYDPDLDGSGDMARGLHLSRHMMHEIAALGLPVATEVLQPMLASY 175
                                               ********************************************************************* PP

                                 TIGR00034 148 ladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaiv 216
                                               + dll+w aiGarttesq+hrelasgl  +vgfkn+t G++ va+dairaaa++h  ++ +++G+ a+ 
  lcl|NCBI__GCF_002151265.1:WP_086509326.1 176 FDDLLAWVAIGARTTESQLHRELASGLEAAVGFKNATSGDVGVAVDAIRAAAHPHQHFGLDEQGRPALR 244
                                               ********************************************************************* PP

                                 TIGR00034 217 etkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqi 284
                                               et+Gn+++h++lrGG++ pn+d+++vae+++ le+agl ++lm+d+sh+n++kd++rq ev ++vv q 
  lcl|NCBI__GCF_002151265.1:WP_086509326.1 245 ETTGNSYAHVVLRGGHHgPNHDSRSVAEARRALEQAGLPARLMVDCSHANARKDHRRQGEVLRDVVTQR 313
                                               ********************************************************************* PP

                                 TIGR00034 285 aeGekaiiGvmiesnleeGnqsl.keelkyGksvtdacigwedteallrklaea 337
                                                +Ge+a++G+m+es+leeG+q+l   +l yG+svtd c+gw+ teall + a+ 
  lcl|NCBI__GCF_002151265.1:WP_086509326.1 314 VQGETALMGLMLESHLEEGRQELaPGALRYGVSVTDPCLGWQATEALLLEAADR 367
                                               ***********************7789********************9888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (369 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: 9.24
//
[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