Alignments for a candidate for aroG in Enterococcus termitis LMG 8895

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Enterococcus termitis LMG 8895

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate WP_069665089.1 BCR25_RS18485 3-deoxy-7-phosphoheptulonate synthase

Query= ecocyc::AROH-MONOMER
         (348 letters)



>NCBI__GCF_001730305.1:WP_069665089.1
          Length = 342

 Score =  189 bits (480), Expect = 9e-53
 Identities = 115/315 (36%), Positives = 177/315 (56%), Gaps = 22/315 (6%)

Query: 40  RRIEKILNGEDKRLLVIIGPCSIHDLTAAMEYATRLQSLRNQYQSRLEIVMRTYFEKPRT 99
           + ++ I+ G+ +++L++IGPCS HD  A MEY TRL  L+ + Q ++ +V R Y  KPRT
Sbjct: 34  QELKNIIEGKSQKILLLIGPCSAHDEDAVMEYVTRLAKLQERVQDKVFMVPRVYTNKPRT 93

Query: 100 -VVGWKGLISDPDLNGSYRVNHGLELARKLLLQV-NELGVPTATEFLDMVTGQFIADLIS 157
              G+KGL+   +  G   +  G+   R L  +V +E  + TA E L     +F+ DL+S
Sbjct: 94  NGDGYKGLLHQQNPEGESNLIQGIAAVRSLHNRVISETSLTTADEMLYPENLEFVEDLVS 153

Query: 158 WGAIGARTTESQIHREMASALSCPVGFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQM 217
           + A+GAR+ E Q HR +AS +  P G KN T GN ++  +++ AA+    F+    NG  
Sbjct: 154 YIAVGARSVEDQQHRFVASGIDQPTGMKNPTSGNLKVLFNSLYAAQQKQEFIF---NGME 210

Query: 218 TIYQTSGNPYGHIIMRGG------KKPNYHADDIAAACDTLH--EFDLPEHLVVDFSHGN 269
              ++S NP  H+++RGG        PNYH +D+    +     ++  P  +V+D +H N
Sbjct: 211 V--ESSANPLAHVVLRGGLNEYGENLPNYHYEDLLKVVEHYKSGQYKNP-FIVIDTNHDN 267

Query: 270 CQKQHRRQLEVC-EDICQQIRNGSTA--IAGIMAESFLREGTQKIVGSQPLTYGQSITDP 326
             KQ++ Q+ +  E +  +  N      + G M ESFL  G Q+  G     +GQSITDP
Sbjct: 268 SGKQYKEQVRIVKETLINRSWNDDMKQWVRGFMIESFLENGRQEANGK---VFGQSITDP 324

Query: 327 CLGWEDTERLVEKLA 341
           CLGW +TERLVE +A
Sbjct: 325 CLGWAETERLVEYIA 339


Lambda     K      H
   0.320    0.135    0.399 

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: 293
Number of extensions: 17
Number of successful extensions: 6
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: 348
Length of database: 342
Length adjustment: 29
Effective length of query: 319
Effective length of database: 313
Effective search space:    99847
Effective search space used:    99847
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 WP_069665089.1 BCR25_RS18485 (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.2279172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.5e-75  238.8   0.0    3.9e-75  238.7   0.0    1.0  1  NCBI__GCF_001730305.1:WP_069665089.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069665089.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.7   0.0   3.9e-75   3.9e-75      16     336 ..      14     340 ..       1     342 [] 0.87

  Alignments for each domain:
  == domain 1  score: 238.7 bits;  conditional E-value: 3.9e-75
                             TIGR00034  16 elkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkddleivmrv 88 
                                           ++k+   lt+++aek a   +e+++i++Gk +++l++iGPcs hd  a +ey +rl+kl+e+++d++ +v rv
  NCBI__GCF_001730305.1:WP_069665089.1  14 QVKSLSKLTTQQAEKKAIRDQELKNIIEGKSQKILLLIGPCSAHDEDAVMEYVTRLAKLQERVQDKVFMVPRV 86 
                                           444455678888888888899**************************************************** PP

                             TIGR00034  89 yfekPrtt.vGWkGlindPdlnesfdvnkGlriarkllldl.velglplatelldtispqyladllswgaiGa 159
                                           y +kPrt   G+kGl+ + + ++  ++ +G++  r l   +  e+ l +a e+l +    ++ dl+s+ a+Ga
  NCBI__GCF_001730305.1:WP_069665089.1  87 YTNKPRTNgDGYKGLLHQQNPEGESNLIQGIAAVRSLHNRViSETSLTTADEMLYPENLEFVEDLVSYIAVGA 159
                                           *******736***************************987527899*************************** PP

                             TIGR00034 160 rttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGG. 231
                                           r+ e q hr +asg+  p g+kn t G+lkv  +++ aa+++  f+     G    ve++ n+ +h++lrGG 
  NCBI__GCF_001730305.1:WP_069665089.1 160 RSVEDQQHRFVASGIDQPTGMKNPTSGNLKVLFNSLYAAQQKQEFIFN---GM--EVESSANPLAHVVLRGGl 227
                                           *********************************************964...33..268899**********75 PP

                             TIGR00034 232 ....kk.pnydaedvaevkeelekaglk.eelmidfshgnsnkdykrqlevaes.vveq.ia.eGekaiiGvm 295
                                               ++ pny+ ed+ +v e+ +  + k + ++id+ h ns k+yk+q+ ++++ ++++  + + ++ + G m
  NCBI__GCF_001730305.1:WP_069665089.1 228 neygENlPNYHYEDLLKVVEHYKSGQYKnPFIVIDTNHDNSGKQYKEQVRIVKEtLINRsWNdDMKQWVRGFM 300
                                           44445689************9998775515699****************998762344413313456799*** PP

                             TIGR00034 296 iesnleeGnqslkeelkyGksvtdacigwedteallrklae 336
                                           ies+le+G+q+ + + ++G+s+td c+gw +te+l++ +ae
  NCBI__GCF_001730305.1:WP_069665089.1 301 IESFLENGRQEAN-GKVFGQSITDPCLGWAETERLVEYIAE 340
                                           **********975.678********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (342 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: 00:00:00.00
# Mc/sec: 13.06
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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