Alignments for a candidate for leuA in Azorhizobium caulinodans ORS 571

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Azorhizobium caulinodans ORS 571

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_012172068.1 AZC_RS18230 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000010525.1:WP_012172068.1
          Length = 526

 Score =  528 bits (1359), Expect = e-154
 Identities = 276/513 (53%), Positives = 360/513 (70%), Gaps = 2/513 (0%)

Query: 4   TNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAI 63
           T+RVIIFDTTLRDGEQ PGA+MT EEK+ VA  LE +GVD+IEAGF  AS GDFE+V  I
Sbjct: 16  TDRVIIFDTTLRDGEQCPGASMTFEEKLEVAELLETMGVDVIEAGFPIASIGDFESVAEI 75

Query: 64  AKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEA 123
           A+    + +  LSRA   DI +  EAV  A + RIHTF++TSP+HM+YKL+ +P QV+E 
Sbjct: 76  ARRSKTAIIAGLSRAALNDIDRCAEAVKQAKRGRIHTFLSTSPVHMKYKLQKEPHQVLEM 135

Query: 124 AVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTE 183
            V +V  AR + +DVE+S ED  R+E+DFL     A I+AGATTINIPDTVGY+ P + E
Sbjct: 136 IVASVTRARNHVEDVEWSAEDGTRTEMDFLCRCVEAAIKAGATTINIPDTVGYTTPQEYE 195

Query: 184 EFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASV 243
             FR +  + PN  K ++S HCHNDLG+AVANSLA L GGARQ+ECT+NG+GERAGNA++
Sbjct: 196 ALFRTVRERVPNSDKAIFSVHCHNDLGMAVANSLAGLAGGARQIECTINGIGERAGNAAL 255

Query: 244 EEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQ 303
           EE+VMA+  R D+    TGID T +  +SK+VS +T +PVQ NKAIVG NAF+HESGIHQ
Sbjct: 256 EEVVMAINTRRDVLPYRTGIDATLLTRASKMVSGVTSFPVQYNKAIVGRNAFAHESGIHQ 315

Query: 304 DGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARF 363
           DG+LKH +TYEIM+ ESVG     L +GK SGR AF+ KL  LG EL  E ALN AF RF
Sbjct: 316 DGMLKHTQTYEIMTPESVGVTKTSLVMGKHSGRAAFRDKLKALGYEL-GENALNDAFTRF 374

Query: 364 KELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKR 423
           K+LAD+K+ I+DED+ ALV D+  +   +  K +S  +   T    RA +   + G+ + 
Sbjct: 375 KDLADRKKVIYDEDIEALV-DQGIAAAYDRVKLLSLSVIAGTRGPQRATMRIEVDGQPRI 433

Query: 424 ASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGA 483
             A G+GPVDA F AI+++    A L++Y V+AVT+GT++Q E SVRLA   +VV  + A
Sbjct: 434 EEAEGNGPVDATFNAIKALIPHTAKLELYQVHAVTEGTDAQAEVSVRLAEDGKVVTARAA 493

Query: 484 DTDVLVATAKAYLSALSKLEFSAAKPKAQGSGT 516
           D D LVA+A+AY++AL+KL        AQ + +
Sbjct: 494 DPDTLVASAQAYITALNKLSVKRQSVNAQAAAS 526


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: 624
Number of extensions: 23
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: 526
Length adjustment: 35
Effective length of query: 482
Effective length of database: 491
Effective search space:   236662
Effective search space used:   236662
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_012172068.1 AZC_RS18230 (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.1873962.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-214  696.9   4.6   7.3e-214  696.7   4.6    1.0  1  NCBI__GCF_000010525.1:WP_012172068.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012172068.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.7   4.6  7.3e-214  7.3e-214       1     494 []      18     510 ..      18     510 .. 0.99

  Alignments for each domain:
  == domain 1  score: 696.7 bits;  conditional E-value: 7.3e-214
                             TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 
                                           rv+ifdttlrdGeq+pgas+t eekl++a+ le +gvd+ieaGfp++s gdfe+v +iar+ k+a+++gl+ra
  NCBI__GCF_000010525.1:WP_012172068.1  18 RVIIFDTTLRDGEQCPGASMTFEEKLEVAELLETMGVDVIEAGFPIASIGDFESVAEIARRSKTAIIAGLSRA 90 
                                           79*********************************************************************** PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                             +did  aea+k+a++ rihtf++ts++h+++kl+k+ ++vle+iv+ v++a+n+v+dve+saed +rte++
  NCBI__GCF_000010525.1:WP_012172068.1  91 ALNDIDRCAEAVKQAKRGRIHTFLSTSPVHMKYKLQKEPHQVLEMIVASVTRARNHVEDVEWSAEDGTRTEMD 163
                                           ************************************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           fl+r veaai+aGattiniPdtvGy++P+ey +l+++++e+vPn dkai+svhch+dlG+avansla +  Ga
  NCBI__GCF_000010525.1:WP_012172068.1 164 FLCRCVEAAIKAGATTINIPDTVGYTTPQEYEALFRTVRERVPNSDKAIFSVHCHNDLGMAVANSLAGLAGGA 236
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292
                                           rq+ectinGiGeraGnaaleevvma+++r+d+l+++tgi+   + r+s++vs +t+ +vq nkaivG nafah
  NCBI__GCF_000010525.1:WP_012172068.1 237 RQIECTINGIGERAGNAALEEVVMAINTRRDVLPYRTGIDATLLTRASKMVSGVTSFPVQYNKAIVGRNAFAH 309
                                           ************************************************************************* PP

                             TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365
                                           esGihqdG+lk+ +tyei++pes+G++k+ lv+gk+sGraa++++l++lG++l e+ l+ +f++fk+lad+kk
  NCBI__GCF_000010525.1:WP_012172068.1 310 ESGIHQDGMLKHTQTYEIMTPESVGVTKTSLVMGKHSGRAAFRDKLKALGYELGENALNDAFTRFKDLADRKK 382
                                           ************************************************************************* PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                            ++ded+ealv + +     +++kl +l+v +g+     at++++v+g+ + + a GnGpvda+++ai+ ++ 
  NCBI__GCF_000010525.1:WP_012172068.1 383 VIYDEDIEALVDQGIA-AAYDRVKLLSLSVIAGTRGPQRATMRIEVDGQPRIEEAEGNGPVDATFNAIKALIP 454
                                           **************99.67778*************************************************** PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                              kl+ y+++a++eg+da++ev+v+l  +gk ++ r+++ d + asa+ay+ aln
  NCBI__GCF_000010525.1:WP_012172068.1 455 HTAKLELYQVHAVTEGTDAQAEVSVRLAEDGKVVTARAADPDTLVASAQAYITALN 510
                                           ******************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (526 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.92
//
[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 2024 update 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 original 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