Alignments for a candidate for aroB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Herbaspirillum seropedicae SmR1

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate HSERO_RS20920 HSERO_RS20920 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>FitnessBrowser__HerbieS:HSERO_RS20920
          Length = 596

 Score =  406 bits (1044), Expect = e-118
 Identities = 211/380 (55%), Positives = 275/380 (72%), Gaps = 6/380 (1%)

Query: 48  SSSNVGRTRLMRASASSTAPVMDTSPTKAVSSAPTIVDVDLGDRSYPIYIGSGLLDQPDL 107
           S+S+  +T    ASA  T   M+ +   A   AP  ++VDLG+RSYPI+IG GLLD   L
Sbjct: 206 STSHTSQTFHGAASAEPTLARMNQNTASA--PAPITLNVDLGERSYPIHIGRGLLDDAGL 263

Query: 108 LQRHVHGKRVLVVTNSTVAPIYLDKVVGALTNGNPNVSVESVILPDGEKYKNMDTLMKVF 167
           L ++V GKRV +VTN  V P+YLDKV   L      V+   ++LPDGE+ KN  +LMK+F
Sbjct: 264 LPQYVKGKRVAIVTNDKVGPLYLDKVAQPLRAAGKLVT--EIVLPDGEEEKNWASLMKIF 321

Query: 168 DKAIESRLDRRCTFVALGGGVIGDMCGYAAASFLRGVNFIQIPTTVMAQVDSSVGGKTGI 227
           D+ +  + DR+ T +ALGGGVIGD+ G+AAAS++RGV F+Q+PTT+++QVDSSVGGKTGI
Sbjct: 322 DRLLADKCDRKTTLIALGGGVIGDLTGFAAASYMRGVPFVQVPTTLLSQVDSSVGGKTGI 381

Query: 228 NHRLGKNLIGAFYQPQCVLIDTDTLNTLPDRELASGLAEVVKYGLIRDANFFEWQEKNMP 287
           NH LGKN+IGAFYQPQ V+ DT TL+TLP REL++G+AEV+K+G I DA FF+W E N+ 
Sbjct: 382 NHPLGKNMIGAFYQPQAVIADTATLHTLPPRELSAGIAEVIKHGAIIDAPFFDWIETNIA 441

Query: 288 ALMARDPSALAYAIKRSCENKAEVVSLDEKESGLRATLNLGHTFGHAIETGFGYGQWLHG 347
            L+++D +ALAYAI+RSCE KAEVV  DE+E GLRA LN GHTFGHAIE G GYGQWLHG
Sbjct: 442 QLVSKDDAALAYAIQRSCEIKAEVVRQDEREGGLRAILNFGHTFGHAIENGLGYGQWLHG 501

Query: 348 EAVAAGMVMAVDMSYRLGWIDESIVNRAHNILQQAKLPTAPPETMTVEMFKSVMAVDKKV 407
           EAV  GMVMA D+S+RLG+ID    +R   +   A LPT  P+ + V  +  +M VDKK 
Sbjct: 502 EAVGCGMVMAADLSHRLGYIDAGARDRVRALTAAAGLPTVAPD-LGVARWLELMEVDKKN 560

Query: 408 ADGLLRLILLKGPLGNCVFT 427
             G ++ IL++ PLG+ + T
Sbjct: 561 EGGQIKFILIR-PLGSPLIT 579


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: 599
Number of extensions: 21
Number of successful extensions: 2
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: 445
Length of database: 596
Length adjustment: 35
Effective length of query: 410
Effective length of database: 561
Effective search space:   230010
Effective search space used:   230010
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 HSERO_RS20920 HSERO_RS20920 (3-dehydroquinate synthase)
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.18346.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.9e-124  401.3   0.0   2.9e-124  400.7   0.0    1.3  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20920  HSERO_RS20920 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20920  HSERO_RS20920 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.7   0.0  2.9e-124  2.9e-124       1     342 [.     249     589 ..     249     591 .. 0.96

  Alignments for each domain:
  == domain 1  score: 400.7 bits;  conditional E-value: 2.9e-124
                                  TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                                y++++g+gll+ +    +  k +++ ++t+++v  l+ +k+++ l+++g  v+++v+pdgee K++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20920 249 YPIHIGRGLLDDAGLLPQYvKGKRVAIVTNDKVGPLYLDKVAQPLRAAGKLVTEIVLPDGEEEKNWAS 316
                                                68999****99665444434569********************************************* PP

                                  TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135
                                                + k+ d+ll+ k++rk++l+a+GGGv+gDl+GF+Aa+y+RG+++vqvPTtll++vDssvGGKtgin+p
  lcl|FitnessBrowser__HerbieS:HSERO_RS20920 317 LMKIFDRLLADKCDRKTTLIALGGGVIGDLTGFAAASYMRGVPFVQVPTTLLSQVDSSVGGKTGINHP 384
                                                ******************************************************************** PP

                                  TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleal 203
                                                lgkN+iGafyqP+aV+ d+++l+tlp rel++G+aEviKhg+i da +f+++e+n ++l+++ + +al
  lcl|FitnessBrowser__HerbieS:HSERO_RS20920 385 LGKNMIGAFYQPQAVIADTATLHTLPPRELSAGIAEVIKHGAIIDAPFFDWIETNIAQLVSK-DDAAL 451
                                                ********************************************************998875.559** PP

                                  TIGR01357 204 eelikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklg 270
                                                + +i+rs+e+KaevV +De+e glRa+LNfGHt+gHaiE+ l+y+ + HGeaV +Gmv++a ls++lg
  lcl|FitnessBrowser__HerbieS:HSERO_RS20920 452 AYAIQRSCEIKAEVVRQDEREGGLRAILNFGHTFGHAIENGLGYGqWLHGEAVGCGMVMAADLSHRLG 519
                                                ********************************************99********************** PP

                                  TIGR01357 271 llkaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteee 338
                                                +++a  ++r++al+ ++glpt  ++ l v   l+ +  DKKneg++ik++l++ +G++ ++ +v+++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS20920 520 YIDAGARDRVRALTAAAGLPTVAPD-LGVARWLELMEVDKKNEGGQIKFILIRPLGSPLIT-NVPQDL 585
                                                ***********************97.********************************999.888887 PP

                                  TIGR01357 339 llea 342
                                                ll++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20920 586 LLQT 589
                                                7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (596 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: 18.14
//
[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