Alignments for a candidate for leuA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Stenotrophomonas chelatiphaga DSM 21508

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_057509301.1 ABB28_RS14490 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_001431535.1:WP_057509301.1
          Length = 527

 Score =  447 bits (1151), Expect = e-130
 Identities = 237/501 (47%), Positives = 332/501 (66%), Gaps = 9/501 (1%)

Query: 6   RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIAK 65
           R+ IFDTTLRDGEQSPG +M+ ++K+ +AR L++LGVD+IE GF A+S  D EA+  I +
Sbjct: 13  RIRIFDTTLRDGEQSPGCSMSPQQKLVMARALDELGVDVIETGFPASSQSDREAMTMIGR 72

Query: 66  TITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAAV 125
            + +  +  LSR +  DI  +  ++  A   R+H F++TSP+H E+KL+M  +QV+E+  
Sbjct: 73  EVQRPVLAVLSRCLAADIETSVRSLDSAAHPRLHVFLSTSPLHREHKLRMTREQVLESVR 132

Query: 126 KAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEEF 185
           K V +AR Y DDVEFS EDA R+E+D+L E+    I AGATTIN+PDTVG++ P +    
Sbjct: 133 KHVALARSYIDDVEFSAEDATRTELDYLIEVSRVAIAAGATTINLPDTVGFTTPEEIRAM 192

Query: 186 FRELIAKTPN---GGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNAS 242
           F+++IA   +     +V++SAHCHNDLGLAVANSLAA++GGARQVECTVNG+GERAGN +
Sbjct: 193 FQQVIAGVADVSGAERVIFSAHCHNDLGLAVANSLAAIEGGARQVECTVNGIGERAGNCA 252

Query: 243 VEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIH 302
           VEEI MALKVR   +  +T I+T +IV +S+L+  + G PVQ NKAIVGANAF+HESGIH
Sbjct: 253 VEEIAMALKVRQAFYDQDTAINTQRIVSTSQLLQRLVGMPVQRNKAIVGANAFAHESGIH 312

Query: 303 QDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFAR 362
           Q G+L+HR TYEIM  E VGW  +++ LG+ SGR A + +L  LG  LE EE L   F +
Sbjct: 313 QHGMLRHRGTYEIMRPEDVGWEDSQMVLGRHSGRAAVEARLRALGFWLEEEE-LKLVFEQ 371

Query: 363 FKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFS-IKGEE 421
           FK L +++R + D DL  L+    G  + + Y+  S  IS + G    A +  S   G  
Sbjct: 372 FKSLCEQQRVVTDSDLQTLM---QGGASTQGYRLASMTIS-DVGSRANALVELSDPDGNR 427

Query: 422 KRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQ 481
              +A G GPVDA+F A+ S       L  Y V++V  G +++GE ++ +  G+ V  G 
Sbjct: 428 VAETAQGDGPVDALFGALSSATGVSLQLDSYQVHSVGIGADARGEANLSVRSGDEVFEGT 487

Query: 482 GADTDVLVATAKAYLSALSKL 502
           G   D++ A+A A+L   ++L
Sbjct: 488 GTSRDIIEASALAWLDVANRL 508


Lambda     K      H
   0.313    0.129    0.352 

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: 606
Number of extensions: 18
Number of successful extensions: 4
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: 517
Length of database: 527
Length adjustment: 35
Effective length of query: 482
Effective length of database: 492
Effective search space:   237144
Effective search space used:   237144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_057509301.1 ABB28_RS14490 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.3330.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-194  630.4   0.2     1e-193  630.3   0.2    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509301.1  ABB28_RS14490 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509301.1  ABB28_RS14490 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.3   0.2    1e-193    1e-193       1     494 []      13     506 ..      13     506 .. 0.97

  Alignments for each domain:
  == domain 1  score: 630.3 bits;  conditional E-value: 1e-193
                                 TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvg 69 
                                               r+ ifdttlrdGeq+pg s++ ++kl +a+al++lgvd+ie+Gfp+ss++d ea+  i rev++++++ 
  lcl|NCBI__GCF_001431535.1:WP_057509301.1  13 RIRIFDTTLRDGEQSPGCSMSPQQKLVMARALDELGVDVIETGFPASSQSDREAMTMIGREVQRPVLAV 81 
                                               799****************************************************************** PP

                                 TIGR00973  70 laravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsae 138
                                               l+r++  di+ ++++l++a++ r+h+f++ts++h+e+kl++t+++vle ++k v+ a++++ddvefsae
  lcl|NCBI__GCF_001431535.1:WP_057509301.1  82 LSRCLAADIETSVRSLDSAAHPRLHVFLSTSPLHREHKLRMTREQVLESVRKHVALARSYIDDVEFSAE 150
                                               ********************************************************************* PP

                                 TIGR00973 139 dagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPni...dkailsvhchddl 204
                                               da+rtel++l++v + ai aGattin+PdtvG+++P+e  ++++++   v ++   +++i+s+hch+dl
  lcl|NCBI__GCF_001431535.1:WP_057509301.1 151 DATRTELDYLIEVSRVAIAAGATTINLPDTVGFTTPEEIRAMFQQVIAGVADVsgaERVIFSAHCHNDL 219
                                               **************************************999999998876655333899********** PP

                                 TIGR00973 205 GlavanslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskl 273
                                               Glavanslaa++ Garqvect+nGiGeraGn+a+ee++malkvr+ f++ +t+int++i  ts+l+ +l
  lcl|NCBI__GCF_001431535.1:WP_057509301.1 220 GLAVANSLAAIEGGARQVECTVNGIGERAGNCAVEEIAMALKVRQAFYDQDTAINTQRIVSTSQLLQRL 288
                                               ********************************************************************* PP

                                 TIGR00973 274 tgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelG 342
                                               +gm+vqrnkaivG+nafahesGihq+G+l+++ tyei++pe++G + +++vlg++sGraa++ rl++lG
  lcl|NCBI__GCF_001431535.1:WP_057509301.1 289 VGMPVQRNKAIVGANAFAHESGIHQHGMLRHRGTYEIMRPEDVGWEDSQMVLGRHSGRAAVEARLRALG 357
                                               ********************************************************************* PP

                                 TIGR00973 343 fkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkv 411
                                               f l+eeel+ +fe+fk l+++++ v+d+dl++l++       +++++l ++ ++    s + a v+l  
  lcl|NCBI__GCF_001431535.1:WP_057509301.1 358 FWLEEEELKLVFEQFKSLCEQQRVVTDSDLQTLMQGGAS---TQGYRLASMTISDVG-SRANALVELSD 422
                                               *********************************998877...789******997655.45889****99 PP

                                 TIGR00973 412 k.geekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvat 479
                                               + g++ +++a+G Gpvda++ a++ +++++ +l  y+++++g g+da ge+++ ++  ++ ++G+g + 
  lcl|NCBI__GCF_001431535.1:WP_057509301.1 423 PdGNRVAETAQGDGPVDALFGALSSATGVSLQLDSYQVHSVGIGADARGEANLSVRSGDEVFEGTGTSR 491
                                               868889*************************************************************** PP

                                 TIGR00973 480 diveasakayvnaln 494
                                               di+easa a++++ n
  lcl|NCBI__GCF_001431535.1:WP_057509301.1 492 DIIEASALAWLDVAN 506
                                               ***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (527 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.67
//
[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