Alignments for a candidate for leuA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Cupriavidus basilensis 4G11

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate RR42_RS05465 RR42_RS05465 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Cup4G11:RR42_RS05465
          Length = 512

 Score =  639 bits (1647), Expect = 0.0
 Identities = 318/506 (62%), Positives = 400/506 (79%), Gaps = 2/506 (0%)

Query: 4   TNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAI 63
           ++++IIFDTTLRDGEQSPGA+MT+EEKIR+ARQLE+L VD+IEAGFAA+S GDFEA+ +I
Sbjct: 2   SDKLIIFDTTLRDGEQSPGASMTREEKIRIARQLERLKVDVIEAGFAASSNGDFEAIRSI 61

Query: 64  AKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEA 123
           A+ +  ST+CSL+RA +RDI +A EA+ PA   RIHTFIATS +HME KL+M P QV E 
Sbjct: 62  AQVVKDSTICSLARANDRDIARAAEALKPANSFRIHTFIATSALHMEKKLRMTPDQVFEQ 121

Query: 124 AVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTE 183
           A++AV+ AR++TDD+EFS ED  RS++DFL  +   VI+ GATTIN+PDTVGY++P    
Sbjct: 122 AIQAVRFARQFTDDIEFSPEDGSRSDMDFLCRVLEGVIKEGATTINLPDTVGYAVPEGYA 181

Query: 184 EFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALK-GGARQVECTVNGLGERAGNAS 242
              R +  + PN  K +WS HCHNDLG+AVANSLAA+K GGARQVECT+NGLGERAGN S
Sbjct: 182 GLIRSVRERIPNSDKAIWSVHCHNDLGMAVANSLAAVKLGGARQVECTINGLGERAGNTS 241

Query: 243 VEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIH 302
           +EE+VMA+K R D F ++ G+DTTQIVP+SKLVS ITG+ VQPNKA+VGANAF+H SGIH
Sbjct: 242 LEEVVMAVKTRRDYFDMDVGVDTTQIVPASKLVSQITGFVVQPNKAVVGANAFAHASGIH 301

Query: 303 QDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFAR 362
           QDGVLK R+TYEIM AE VGW+ N++ LGKLSGRNAFK +L +LGIELESE  +NAAF R
Sbjct: 302 QDGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIELESEGEVNAAFTR 361

Query: 363 FKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEK 422
           FKELAD+K EIFDED+ A+VSDE   +N E ++FIS    +ETGE P A +VF++ G E 
Sbjct: 362 FKELADQKSEIFDEDIMAIVSDEAHDVN-EHFRFISLSQHSETGERPHARVVFNMDGNEV 420

Query: 423 RASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQG 482
                G+GPVDA   AIE    SGA L +YSVNA+T GT++QGE +VRL++G R+VNG G
Sbjct: 421 TGEGEGNGPVDATLHAIEGKVASGAELVLYSVNAITAGTQAQGEVTVRLSKGGRIVNGVG 480

Query: 483 ADTDVLVATAKAYLSALSKLEFSAAK 508
            D D++ A+AKAYL+AL+KL   A +
Sbjct: 481 TDPDIVAASAKAYLAALNKLHDKAVQ 506


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: 695
Number of extensions: 18
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: 517
Length of database: 512
Length adjustment: 35
Effective length of query: 482
Effective length of database: 477
Effective search space:   229914
Effective search space used:   229914
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 RR42_RS05465 RR42_RS05465 (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.6387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-216  705.1   5.2   2.3e-216  704.9   5.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05465  RR42_RS05465 2-isopropylmalate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05465  RR42_RS05465 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  704.9   5.2  2.3e-216  2.3e-216       1     494 []       4     498 ..       4     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 704.9 bits;  conditional E-value: 2.3e-216
                                 TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvg 69 
                                               +++ifdttlrdGeq+pgas+t eek++ia++lerl vd+ieaGf++ss+gdfea++ ia+ vk++++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465   4 KLIIFDTTLRDGEQSPGASMTREEKIRIARQLERLKVDVIEAGFAASSNGDFEAIRSIAQVVKDSTICS 72 
                                               689****************************************************************** PP

                                 TIGR00973  70 laravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsae 138
                                               lara ++di  aaealkpa+ +rihtfiats++h+e+kl++t d+v e++++av++a++f+dd+efs+e
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465  73 LARANDRDIARAAEALKPANSFRIHTFIATSALHMEKKLRMTPDQVFEQAIQAVRFARQFTDDIEFSPE 141
                                               ********************************************************************* PP

                                 TIGR00973 139 dagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGla 207
                                               d +r++++fl+rv+e +i+ Gattin+PdtvGya+P+ y+ li++++e++Pn dkai svhch+dlG+a
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465 142 DGSRSDMDFLCRVLEGVIKEGATTINLPDTVGYAVPEGYAGLIRSVRERIPNSDKAIWSVHCHNDLGMA 210
                                               ********************************************************************* PP

                                 TIGR00973 208 vanslaavkn.GarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltg 275
                                               vanslaavk  GarqvectinG+GeraGn++leevvma+k+r+d++++++g++t +i  +s+lvs++tg
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465 211 VANSLAAVKLgGARQVECTINGLGERAGNTSLEEVVMAVKTRRDYFDMDVGVDTTQIVPASKLVSQITG 279
                                               ********9637********************************************************* PP

                                 TIGR00973 276 mlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfk 344
                                                +vq+nka+vG+nafah sGihqdGvlk + tyei+++e++G +++k+vlgk sGr+a+k+rl+elG++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465 280 FVVQPNKAVVGANAFAHASGIHQDGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIE 348
                                               ********************************************************************* PP

                                 TIGR00973 345 ldee.eldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvk 412
                                               l++e e++ +f++fkelad+k e+fded++a+v++e + + +e++++ +l+ +s + + p a v ++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465 349 LESEgEVNAAFTRFKELADQKSEIFDEDIMAIVSDEAH-DVNEHFRFISLSQHSETGERPHARVVFNMD 416
                                               875549******************************98.78888************************* PP

                                 TIGR00973 413 geekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdi 481
                                               g+e +    GnGpvda+++aie  +    +l+ ys++a + g++a+gev+v+l   g+ ++G+g + di
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465 417 GNEVTGEGEGNGPVDATLHAIEGKVASGAELVLYSVNAITAGTQAQGEVTVRLSKGGRIVNGVGTDPDI 485
                                               ********************************************************************* PP

                                 TIGR00973 482 veasakayvnaln 494
                                               v asakay+ aln
  lcl|FitnessBrowser__Cup4G11:RR42_RS05465 486 VAASAKAYLAALN 498
                                               ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (512 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.09
//
[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