Alignments for a candidate for aroB in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Herbaspirillum autotrophicum IAM 14942

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_050464609.1 AKL27_RS19905 bifunctional shikimate kinase/3-dehydroquinate synthase AroKB

Query= SwissProt::Q8RU74
         (442 letters)



>NCBI__GCF_001189915.1:WP_050464609.1
          Length = 561

 Score =  408 bits (1048), Expect = e-118
 Identities = 212/370 (57%), Positives = 269/370 (72%), Gaps = 5/370 (1%)

Query: 69  SSSKASSQAPTVVEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLD 128
           S+  A+  +   ++V+LG RSYPI IG  LLD P+LL RHIHGKRV +VTN  V PLYL+
Sbjct: 193 STMNAAPSSAIALQVELGERSYPITIGHQLLDNPELLTRHIHGKRVAIVTNDIVGPLYLE 252

Query: 129 KTISALTDGNPNVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGD 188
           +  S L      VT   ++LPDGE  KN  +LMK+FD  +  + DR+ T VALGGGVIGD
Sbjct: 253 RVSSLLRAAGKQVT--EIVLPDGEGEKNWASLMKIFDVLLAEQCDRKTTLVALGGGVIGD 310

Query: 189 MCGYAAASYLRGVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDT 248
           + G+AAASY+RGV F+Q+PTT+++QVDSSVGGKTGINHPLGKNMIGAFYQPQ VL DT T
Sbjct: 311 LTGFAAASYMRGVPFVQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPQAVLADTAT 370

Query: 249 LNTLPDRELASGLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADV 308
           L+TLP RELA+GLAEVIK+G I DA +F+W E N+  L+ARD  A  YAIKRSCE KA+V
Sbjct: 371 LHTLPPRELAAGLAEVIKHGAIIDAPYFDWIEANIEQLVARDNAALAYAIKRSCEIKAEV 430

Query: 309 VSQDEKESGVRATLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSL 368
           V QDE+E G+RA LN GHTFGHA+E G+GYGQWLHGEAV  G +MA D+S RLG+ID + 
Sbjct: 431 VRQDEREGGLRAILNFGHTFGHAIENGLGYGQWLHGEAVGCGMIMAADLSLRLGFIDAAA 490

Query: 369 VQRVQKILQQAKLPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYD 428
             R+  +++ A LPT  P+ +  E +  +M VDKK   G+++ IL+K  LG  + T    
Sbjct: 491 KARLSALVKAAGLPTMAPD-LGQERWLELMQVDKKNEGGEIKFILIK-PLGTPLIT-HAP 547

Query: 429 QKALDETLRA 438
           Q+ L +T+ A
Sbjct: 548 QEILLQTIAA 557


Lambda     K      H
   0.318    0.133    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: 566
Number of extensions: 25
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: 442
Length of database: 561
Length adjustment: 34
Effective length of query: 408
Effective length of database: 527
Effective search space:   215016
Effective search space used:   215016
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_050464609.1 AKL27_RS19905 (bifunctional shikimate kinase/3-dehydroquinate synthase AroKB)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.1441714.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     9e-123  395.8   0.0   1.4e-122  395.2   0.0    1.2  1  NCBI__GCF_001189915.1:WP_050464609.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050464609.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.2   0.0  1.4e-122  1.4e-122       1     340 [.     214     552 ..     214     556 .. 0.95

  Alignments for each domain:
  == domain 1  score: 395.2 bits;  conditional E-value: 1.4e-122
                             TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakll 72 
                                           y++++g++ll++    +++ + +++ ++t++ v  l+ e+++++l+++g +v+++v+pdge  K+++++ k+ 
  NCBI__GCF_001189915.1:WP_050464609.1 214 YPITIGHQLLDNPELLTRHiHGKRVAIVTNDIVGPLYLERVSSLLRAAGKQVTEIVLPDGEGEKNWASLMKIF 286
                                           67999999999665555554569************************************************** PP

                             TIGR01357  73 dqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafy 145
                                           d ll+e+++rk++lva+GGGv+gDl+GF+Aa+y+RG+++vqvPTtll++vDssvGGKtgin+plgkN+iGafy
  NCBI__GCF_001189915.1:WP_050464609.1 287 DVLLAEQCDRKTTLVALGGGVIGDLTGFAAASYMRGVPFVQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFY 359
                                           ************************************************************************* PP

                             TIGR01357 146 qPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevV 218
                                           qP+aVl d+++l+tlp rel++G+aEviKhg+i da  f+++e n ++l+ + +++al+ +ikrs+e+KaevV
  NCBI__GCF_001189915.1:WP_050464609.1 360 QPQAVLADTATLHTLPPRELAAGLAEVIKHGAIIDAPYFDWIEANIEQLVAR-DNAALAYAIKRSCEIKAEVV 431
                                           ***********************************************99976.55****************** PP

                             TIGR01357 219 eeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglp 290
                                            +De+e glRa+LNfGHt+gHaiE+ l+y+ + HGeaV +Gm+++a ls +lg+++a    rl al+k++glp
  NCBI__GCF_001189915.1:WP_050464609.1 432 RQDEREGGLRAILNFGHTFGHAIENGLGYGqWLHGEAVGCGMIMAADLSLRLGFIDAAAKARLSALVKAAGLP 504
                                           *****************************99****************************************** PP

                             TIGR01357 291 tklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340
                                           t  ++ l  e  l+ ++ DKKneg++ik++l++ +G + ++ + ++e ll
  NCBI__GCF_001189915.1:WP_050464609.1 505 TMAPD-LGQERWLELMQVDKKNEGGEIKFILIKPLGTPLIT-HAPQEILL 552
                                           **997.*******************************9988.66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (561 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: 19.10
//
[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