Alignments for a candidate for leuA in Trichlorobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Trichlorobacter lovleyi SZ

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_012471355.1 GLOV_RS16455 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000020385.1:WP_012471355.1
          Length = 519

 Score =  518 bits (1333), Expect = e-151
 Identities = 270/501 (53%), Positives = 362/501 (72%), Gaps = 4/501 (0%)

Query: 3   QTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNA 62
           +T  + IFDTTLRDGEQ+PG +M  EEK+R A+QL+KL VD+IEAGF  AS GDFEAV  
Sbjct: 11  ETRTIKIFDTTLRDGEQAPGNSMNIEEKLRFAKQLQKLNVDVIEAGFPIASEGDFEAVKK 70

Query: 63  IAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKK-RIHTFIATSPIHMEYKLKMKPKQVI 121
           +A++I    +  L R+  +DI +A EA+  A +K RIHTFIATS IHM+YKL+M+P QV+
Sbjct: 71  VAQSIKGPEIAGLCRSNLKDIDRAWEALKYAGEKGRIHTFIATSDIHMKYKLQMEPAQVL 130

Query: 122 EAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYK 181
           E+AVKAVK A  YT +VEFSCEDA+R+++ FLA++  AVI AGATT+NIPDTVGY++P++
Sbjct: 131 ESAVKAVKRAAGYTPNVEFSCEDAVRTQLPFLAQVVEAVIAAGATTVNIPDTVGYTVPFE 190

Query: 182 TEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNA 241
                + L    PN  K V S HCHNDLGL+VANS+AA++ GA QVECT+NG+GERAGN 
Sbjct: 191 YFNIIKYLKDNVPNIEKAVISVHCHNDLGLSVANSIAAIQAGAGQVECTINGIGERAGNC 250

Query: 242 SVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGI 301
           S+EE VM L+ R D+    TGI T Q+ P+S+L++ ITG  VQPNK++VGANAF+HE+GI
Sbjct: 251 SLEEFVMILRTRRDILPFVTGIATEQLTPASRLLTNITGIAVQPNKSVVGANAFAHEAGI 310

Query: 302 HQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFA 361
           HQ G+L  + TYEIM+ ESVG   + L LGK SGR+AFK +L +LG +L+ +E LN AF 
Sbjct: 311 HQHGMLMDKSTYEIMTPESVGLTASALVLGKHSGRHAFKKRLEELGHDLD-DEMLNRAFE 369

Query: 362 RFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEE 421
           RFK LAD K+E+FDEDL A+V+DE  S   + YK     ++  +     A +   I G+ 
Sbjct: 370 RFKALADLKKEVFDEDLDAIVTDE--SREEDQYKLEHITVTCGSFAVATATVQMEINGKP 427

Query: 422 KRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQ 481
            R +  G GPVD+ FKAI  + ++ A L  Y+V ++T GT++QGE +VR+  G   V G+
Sbjct: 428 VRTAELGDGPVDSAFKAIRKLTKTKAKLTQYNVGSITGGTDAQGEVTVRVEEGGHTVVGK 487

Query: 482 GADTDVLVATAKAYLSALSKL 502
           GA TD++VA+AKAY+ AL++L
Sbjct: 488 GASTDIIVASAKAYIHALNRL 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: 610
Number of extensions: 20
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: 519
Length adjustment: 35
Effective length of query: 482
Effective length of database: 484
Effective search space:   233288
Effective search space used:   233288
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_012471355.1 GLOV_RS16455 (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.2856297.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.9e-228  742.4   6.1   1.1e-227  742.2   6.1    1.0  1  NCBI__GCF_000020385.1:WP_012471355.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020385.1:WP_012471355.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.2   6.1  1.1e-227  1.1e-227       2     494 .]      15     506 ..      14     506 .. 0.99

  Alignments for each domain:
  == domain 1  score: 742.2 bits;  conditional E-value: 1.1e-227
                             TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglarav 74 
                                           ++ifdttlrdGeqapg s+++eekl+ ak+l++l+vd+ieaGfp++s+gdfeav+k+a+++k ++++gl+r+ 
  NCBI__GCF_000020385.1:WP_012471355.1  15 IKIFDTTLRDGEQAPGNSMNIEEKLRFAKQLQKLNVDVIEAGFPIASEGDFEAVKKVAQSIKGPEIAGLCRSN 87 
                                           89*********************************************************************** PP

                             TIGR00973  75 ekdidaaaealk.paekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                            kdid a+ealk  +ek rihtfiatsdih+++kl+++ ++vle +vkavk+a  ++++vefs+eda rt+l+
  NCBI__GCF_000020385.1:WP_012471355.1  88 LKDIDRAWEALKyAGEKGRIHTFIATSDIHMKYKLQMEPAQVLESAVKAVKRAAGYTPNVEFSCEDAVRTQLP 160
                                           ************667999******************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           fla+vvea+i aGatt+niPdtvGy++P ey ++ik+lk+nvPni+ka++svhch+dlGl+vans+aa+++Ga
  NCBI__GCF_000020385.1:WP_012471355.1 161 FLAQVVEAVIAAGATTVNIPDTVGYTVPFEYFNIIKYLKDNVPNIEKAVISVHCHNDLGLSVANSIAAIQAGA 233
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292
                                            qvectinGiGeraGn++lee+vm+l++r+d+l+  tgi t+++  +srl++++tg++vq+nk++vG+nafah
  NCBI__GCF_000020385.1:WP_012471355.1 234 GQVECTINGIGERAGNCSLEEFVMILRTRRDILPFVTGIATEQLTPASRLLTNITGIAVQPNKSVVGANAFAH 306
                                           ************************************************************************* PP

                             TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365
                                           e+Gihq+G+l +k+tyei++pes+Gl++++lvlgk+sGr+a+kkrleelG++ld+e l+++fe+fk lad kk
  NCBI__GCF_000020385.1:WP_012471355.1 307 EAGIHQHGMLMDKSTYEIMTPESVGLTASALVLGKHSGRHAFKKRLEELGHDLDDEMLNRAFERFKALADLKK 379
                                           ************************************************************************* PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                           evfdedl a+v++e r  ee+++kle++ v +g+  v+tatv+++++g+  ++a+ G Gpvd+ +kai k+++
  NCBI__GCF_000020385.1:WP_012471355.1 380 EVFDEDLDAIVTDESR--EEDQYKLEHITVTCGSFAVATATVQMEINGKPVRTAELGDGPVDSAFKAIRKLTK 450
                                           **************99..55679*************************99*********************** PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                           ++ kl++y++ + + g+da+gev+v++e  g+++ G+g++tdi+ asakay++aln
  NCBI__GCF_000020385.1:WP_012471355.1 451 TKAKLTQYNVGSITGGTDAQGEVTVRVEEGGHTVVGKGASTDIIVASAKAYIHALN 506
                                           *******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (519 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: 00:00:00.01
# Mc/sec: 16.92
//
[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 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