Alignments for a candidate for leuA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Acidovorax sp. GW101-3H11

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate Ac3H11_530 2-isopropylmalate synthase (EC 2.3.3.13)

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_530
          Length = 512

 Score =  632 bits (1630), Expect = 0.0
 Identities = 321/510 (62%), Positives = 397/510 (77%), Gaps = 1/510 (0%)

Query: 5   NRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIA 64
           +++IIFDTTLRDGEQSPGA+MTK+EK+R+ARQLE+L VD+IEAGFAA+S GDFEAV AIA
Sbjct: 3   DKLIIFDTTLRDGEQSPGASMTKDEKLRIARQLERLKVDVIEAGFAASSNGDFEAVQAIA 62

Query: 65  KTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAA 124
             I  ST+CSLSRA +RDI +A EA+  A   RIHTFIATS +HME KL+M P+QV+E A
Sbjct: 63  NAIKDSTICSLSRANDRDISRAAEALRGANSARIHTFIATSALHMEKKLRMTPEQVLEQA 122

Query: 125 VKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEE 184
            ++V+ AR    D+EFS ED  RS+ DFL  +  AVI  GATTIN+PDTVGY++P     
Sbjct: 123 KQSVRFARNLVADIEFSPEDGYRSDPDFLCRVLEAVITEGATTINVPDTVGYAVPELYGN 182

Query: 185 FFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALK-GGARQVECTVNGLGERAGNASV 243
           F + L  + PN  K +WS HCHNDLG+AVANSLA +K GGARQVECT+NGLGERAGN S+
Sbjct: 183 FIKTLRERIPNSDKAIWSVHCHNDLGMAVANSLAGVKIGGARQVECTINGLGERAGNCSL 242

Query: 244 EEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQ 303
           EEIVMA+K R D FGL+  IDT  IV +S++VS  TG+ VQPNKA+VGANAF+H SGIHQ
Sbjct: 243 EEIVMAVKTRKDYFGLDLAIDTQHIVAASRMVSQTTGFVVQPNKAVVGANAFAHASGIHQ 302

Query: 304 DGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARF 363
           DGVLK R+TYEIM AE VGW+ N++ LGKLSGRNAFK +L +LG++L+SE  +N AFA+F
Sbjct: 303 DGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGVQLDSETEINVAFAKF 362

Query: 364 KELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKR 423
           KELAD+K EIFDED+ ALVSDE  +   E Y F+S    +ETGE+PRA IVF++ G+E R
Sbjct: 363 KELADRKSEIFDEDILALVSDESVTAEKEQYGFVSLFQQSETGEQPRARIVFTVDGQEVR 422

Query: 424 ASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGA 483
             + G+GPVDA  KAIES  +SGA + +YSVNA++  TESQGE +VRL    RVVNG GA
Sbjct: 423 GESDGNGPVDASLKAIESHVKSGAEMVLYSVNAISGSTESQGEVTVRLQNSGRVVNGVGA 482

Query: 484 DTDVLVATAKAYLSALSKLEFSAAKPKAQG 513
           D D++VA+AKAYLSAL+KL+  A +  AQG
Sbjct: 483 DPDIVVASAKAYLSALNKLQSKADRVAAQG 512


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: 656
Number of extensions: 19
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: 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 Ac3H11_530 (2-isopropylmalate synthase (EC 2.3.3.13))
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.22627.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.1e-214  699.4   5.3   1.3e-214  699.2   5.3    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530  2-isopropylmalate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530  2-isopropylmalate synthase (EC 2.3.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.2   5.3  1.3e-214  1.3e-214       1     494 []       4     499 ..       4     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 699.2 bits;  conditional E-value: 1.3e-214
                                       TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevk 63 
                                                     +++ifdttlrdGeq+pgas+t +ekl+ia++lerl vd+ieaGf++ss+gdfeavq ia+++k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530   4 KLIIFDTTLRDGEQSPGASMTKDEKLRIARQLERLKVDVIEAGFAASSNGDFEAVQAIANAIK 66 
                                                     689************************************************************ PP

                                       TIGR00973  64 narvvglaravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkya 126
                                                     ++++++l+ra ++di  aaeal+ a+  rihtfiats++h+e+kl++t ++vle++++ v++a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530  67 DSTICSLSRANDRDISRAAEALRGANSARIHTFIATSALHMEKKLRMTPEQVLEQAKQSVRFA 129
                                                     *************************************************************** PP

                                       TIGR00973 127 knfvddvefsaedagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvP 189
                                                     +n+v d+efs+ed  r++ +fl+rv+ea+i  Gattin+PdtvGya+P+ yg++ik+l+e++P
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 130 RNLVADIEFSPEDGYRSDPDFLCRVLEAVITEGATTINVPDTVGYAVPELYGNFIKTLRERIP 192
                                                     *************************************************************** PP

                                       TIGR00973 190 nidkailsvhchddlGlavanslaavkn.GarqvectinGiGeraGnaaleevvmalkvrkdf 251
                                                     n dkai svhch+dlG+avansla vk  GarqvectinG+GeraGn++lee+vma+k+rkd+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 193 NSDKAIWSVHCHNDLGMAVANSLAGVKIgGARQVECTINGLGERAGNCSLEEIVMAVKTRKDY 255
                                                     **************************9637********************************* PP

                                       TIGR00973 252 lnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspe 314
                                                     ++++++i+t++i ++sr+vs+ tg +vq+nka+vG+nafah sGihqdGvlk + tyei+++e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 256 FGLDLAIDTQHIVAASRMVSQTTGFVVQPNKAVVGANAFAHASGIHQDGVLKARDTYEIMRAE 318
                                                     *************************************************************** PP

                                       TIGR00973 315 siGlkkeklvlgkrsGraalkkrleelGfkld.eeeldklfekfkeladkkkevfdedlealv 376
                                                     ++G +++k+vlgk sGr+a+k+rl+elG++ld e+e++ +f kfkelad+k e+fded+ alv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 319 DVGWSANKIVLGKLSGRNAFKQRLQELGVQLDsETEINVAFAKFKELADRKSEIFDEDILALV 381
                                                     ******************************972579*************************** PP

                                       TIGR00973 377 leelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilel 439
                                                     ++e ++ e+e++ +++l  qs + + p a + + v+g+e +  + GnGpvda +kaie  ++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 382 SDESVTAEKEQYGFVSLFQQSETGEQPRARIVFTVDGQEVRGESDGNGPVDASLKAIESHVKS 444
                                                     ***************************************99999******************* PP

                                       TIGR00973 440 evklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                                       +++ ys++a + +++++gev+v+l+  g+ ++G+g++ div asakay+ aln
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 445 GAEMVLYSVNAISGSTESQGEVTVRLQNSGRVVNGVGADPDIVVASAKAYLSALN 499
                                                     *****************************************************99 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 12.59
//
[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