Alignments for a candidate for aroG in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Halorhodospira halophila SL1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011813795.1 HHAL_RS05085 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P00888
         (356 letters)



>NCBI__GCF_000015585.1:WP_011813795.1
          Length = 358

 Score =  408 bits (1048), Expect = e-118
 Identities = 195/353 (55%), Positives = 256/353 (72%)

Query: 2   QKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGP 61
           + D +N+V++   + L +P ++K+  PL+      + D R+ + DI+ G+D R+  V GP
Sbjct: 3   ESDHVNDVNVATGERLPSPAEIKSEVPLTDAARQTVLDGRQVLRDILDGKDQRIFAVVGP 62

Query: 62  CSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVE 121
           CSIHDPE AL+YARR KAL  E+SD +YLVMRVYFEKPRTT GWKGLINDP MD SF ++
Sbjct: 63  CSIHDPEAALDYARRLKALHDELSDHIYLVMRVYFEKPRTTTGWKGLINDPDMDDSFRID 122

Query: 122 AGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLS 181
            GL++ R+LL E+  MGLP ATEALDP +PQY GDL SW+AIGARTTESQTHREMASGLS
Sbjct: 123 KGLRMGRELLREIAAMGLPTATEALDPYAPQYYGDLVSWTAIGARTTESQTHREMASGLS 182

Query: 182 MPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAPN 241
            PVGFKN TDGS   AINA+++AA PH F+GI+Q G++ +++T+GN  GHV+LRGG  PN
Sbjct: 183 TPVGFKNATDGSQTVAINALQSAASPHSFLGIDQEGRITVIRTRGNQYGHVVLRGGAQPN 242

Query: 242 YSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLM 301
           Y    +  CE+ +E+AG+   ++VDCSH NSNKD   Q  V E V+ Q+++GNRSI+G+M
Sbjct: 243 YDSVSIRLCEQALEKAGMPLRVVVDCSHSNSNKDPGLQSMVLEDVIRQLREGNRSIVGVM 302

Query: 302 IESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           +ESNI  G+Q        + YG+S+TDACI WE T+ +LR+    L G L  R
Sbjct: 303 LESNIGWGSQKLGADPGALDYGISITDACIDWETTEQVLRDAAGQLRGSLRER 355


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: 441
Number of extensions: 11
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: 356
Length of database: 358
Length adjustment: 29
Effective length of query: 327
Effective length of database: 329
Effective search space:   107583
Effective search space used:   107583
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_011813795.1 HHAL_RS05085 (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.1812308.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-148  477.6   0.0   1.1e-147  477.3   0.0    1.0  1  NCBI__GCF_000015585.1:WP_011813795.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_011813795.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.3   0.0  1.1e-147  1.1e-147       2     339 ..       9     349 ..       8     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 477.3 bits;  conditional E-value: 1.1e-147
                             TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkl 74 
                                           d+++++ ++l +P+e+k+++plt +a ++v + r+ + dil+Gkd+r++ v+GPcsihdpeaal+ya+rlk+l
  NCBI__GCF_000015585.1:WP_011813795.1   9 DVNVATGERLPSPAEIKSEVPLTDAARQTVLDGRQVLRDILDGKDQRIFAVVGPCSIHDPEAALDYARRLKAL 81 
                                           677888899**************************************************************** PP

                             TIGR00034  75 aeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqy 147
                                            ++l+d++++vmrvyfekPrtt GWkGlindPd+++sf+++kGlr+ r+ll +++ +glp+ate+ld+ +pqy
  NCBI__GCF_000015585.1:WP_011813795.1  82 HDELSDHIYLVMRVYFEKPRTTTGWKGLINDPDMDDSFRIDKGLRMGRELLREIAAMGLPTATEALDPYAPQY 154
                                           ************************************************************************* PP

                             TIGR00034 148 ladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkG 220
                                           ++dl+sw+aiGarttesq+hre+asgls pvgfkn+tdGs  vai+a+++aa++h fl+++++G++++++t+G
  NCBI__GCF_000015585.1:WP_011813795.1 155 YGDLVSWTAIGARTTESQTHREMASGLSTPVGFKNATDGSQTVAINALQSAASPHSFLGIDQEGRITVIRTRG 227
                                           ************************************************************************* PP

                             TIGR00034 221 nedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiG 293
                                           n++gh++lrGG +pnyd+ ++  +++ lekag+  ++++d+sh+nsnkd   q  v e+v++q++eG+++i+G
  NCBI__GCF_000015585.1:WP_011813795.1 228 NQYGHVVLRGGAQPNYDSVSIRLCEQALEKAGMPLRVVVDCSHSNSNKDPGLQSMVLEDVIRQLREGNRSIVG 300
                                           ************************************************************************* PP

                             TIGR00034 294 vmiesnleeGnqslke...elkyGksvtdacigwedteallrklaeavk 339
                                           vm+esn+  G+q+l++   +l yG s+tdaci+we+te++lr+ a +++
  NCBI__GCF_000015585.1:WP_011813795.1 301 VMLESNIGWGSQKLGAdpgALDYGISITDACIDWETTEQVLRDAAGQLR 349
                                           **************6423369*********************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (358 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.03
//
[ok]

This GapMind analysis is from Jul 25 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 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