Alignments for a candidate for leuA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Caulobacter crescentus NA1000

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate CCNA_01610 CCNA_01610 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Caulo:CCNA_01610
          Length = 524

 Score =  533 bits (1372), Expect = e-156
 Identities = 280/517 (54%), Positives = 366/517 (70%), Gaps = 5/517 (0%)

Query: 1   MTQTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAV 60
           +++ + V++FDTT+RDGEQSPGA+M+ EEK+ +A+ LE++GVD+IEAGF  AS GDFEAV
Sbjct: 9   ISKRDNVVVFDTTMRDGEQSPGASMSLEEKLELAKILEEMGVDVIEAGFPIASNGDFEAV 68

Query: 61  NAIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQV 120
             IA+ IT+STVC L+RA   DI +  EAV  A + RIHTFI+TSP+HM+YKL+M+P  V
Sbjct: 69  RQIAELITESTVCGLARAAAGDIDRCAEAVRRAKRGRIHTFISTSPVHMKYKLQMEPDAV 128

Query: 121 IEAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPY 180
           +EA  ++V  AR    DVE+S EDA R+E DFL     A I+AGATTIN+PDTVGYS P 
Sbjct: 129 LEAITRSVSHARNLVGDVEWSAEDATRTERDFLKRCVEAAIKAGATTINLPDTVGYSYPS 188

Query: 181 KTEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGN 240
           +  E FR++I   P   K ++SAHCHNDLGLAVANS+AA++GGARQVE  +NG+GERAGN
Sbjct: 189 EYGELFRDVITSVPGADKAIFSAHCHNDLGLAVANSIAAIEGGARQVEVAINGIGERAGN 248

Query: 241 ASVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESG 300
           A++EEIVMAL+VR D     T +D   I  +S+ VS ITG+PVQ NKAIVG NAF+HESG
Sbjct: 249 AALEEIVMALRVRGDHLPYGTSVDPVHITRASRYVSAITGFPVQFNKAIVGKNAFAHESG 308

Query: 301 IHQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAF 360
           IHQDG+LK+ ETYEIM  E VG     L +GK SGR+AF+ KL  LG EL  + ALN AF
Sbjct: 309 IHQDGMLKNAETYEIMKPEDVGQGATNLVMGKHSGRHAFREKLKALGYEL-GQNALNDAF 367

Query: 361 ARFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGE 420
            RFKELADKK+ +FD+D+ ALV D + +  +E  +    ++   T +   A++   I G 
Sbjct: 368 GRFKELADKKKHVFDDDIVALVDDAL-ARGSEKIRVSRLRVVAGT-DGQSAELTLDIDGV 425

Query: 421 EKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNG 480
              A ATG GPVDA+F AI  +    AAL+++ V+AVT+GT++Q + SVRL    R+  G
Sbjct: 426 ASTAEATGDGPVDAVFNAIHKIVPHSAALRLFQVHAVTEGTDAQAQVSVRLEEDGRIATG 485

Query: 481 QGADTDVLVATAKAYLSALSKLEFSAAKPKAQGSGTI 517
             ADTD L A+AKAY++AL+ L   A K K++    I
Sbjct: 486 AAADTDTLTASAKAYVNALNNL--FARKEKSRPEAAI 520


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: 659
Number of extensions: 34
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: 524
Length adjustment: 35
Effective length of query: 482
Effective length of database: 489
Effective search space:   235698
Effective search space used:   235698
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 CCNA_01610 CCNA_01610 (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.2793171.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-213  693.1   6.1     1e-212  692.9   6.1    1.0  1  FitnessBrowser__Caulo:CCNA_01610  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_01610  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.9   6.1    1e-212    1e-212       2     494 .]      15     505 ..      14     505 .. 0.99

  Alignments for each domain:
  == domain 1  score: 692.9 bits;  conditional E-value: 1e-212
                         TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdi 78 
                                       v++fdtt+rdGeq+pgas+++eekl++ak le++gvd+ieaGfp++s+gdfeav++ia+ + +++v+glara   di
  FitnessBrowser__Caulo:CCNA_01610  15 VVVFDTTMRDGEQSPGASMSLEEKLELAKILEEMGVDVIEAGFPIASNGDFEAVRQIAELITESTVCGLARAAAGDI 91 
                                       899************************************************************************** PP

                         TIGR00973  79 daaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaa 155
                                       d  aea++ a++ rihtfi+ts++h+++kl+++ d vle i++ v++a+n+v dve+saeda+rte++fl r veaa
  FitnessBrowser__Caulo:CCNA_01610  92 DRCAEAVRRAKRGRIHTFISTSPVHMKYKLQMEPDAVLEAITRSVSHARNLVGDVEWSAEDATRTERDFLKRCVEAA 168
                                       ***************************************************************************** PP

                         TIGR00973 156 ieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGer 232
                                       i+aGattin+PdtvGy  P+eygel++++  +vP+ dkai+s+hch+dlGlavans+aa++ Garqve++inGiGer
  FitnessBrowser__Caulo:CCNA_01610 169 IKAGATTINLPDTVGYSYPSEYGELFRDVITSVPGADKAIFSAHCHNDLGLAVANSIAAIEGGARQVEVAINGIGER 245
                                       ***************************************************************************** PP

                         TIGR00973 233 aGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketye 309
                                       aGnaalee+vmal+vr d l++ t+++  +i r+sr vs +tg +vq nkaivG+nafahesGihqdG+lkn etye
  FitnessBrowser__Caulo:CCNA_01610 246 AGNAALEEIVMALRVRGDHLPYGTSVDPVHITRASRYVSAITGFPVQFNKAIVGKNAFAHESGIHQDGMLKNAETYE 322
                                       ***************************************************************************** PP

                         TIGR00973 310 ilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeee 386
                                       i++pe++G  +++lv+gk+sGr+a++++l++lG++l ++ l+ +f +fkeladkkk+vfd+d++alv + l + +e+
  FitnessBrowser__Caulo:CCNA_01610 323 IMKPEDVGQGATNLVMGKHSGRHAFREKLKALGYELGQNALNDAFGRFKELADKKKHVFDDDIVALVDDALARGSEK 399
                                       **********************************************************************9977665 PP

                         TIGR00973 387 klkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkv 463
                                        +++ +l+v +g++    a ++l ++g  ++a atG Gpvdav++ai+ki+  +  l  ++++a++eg+da+++v+v
  FitnessBrowser__Caulo:CCNA_01610 400 -IRVSRLRVVAGTDG-QSAELTLDIDGVASTAEATGDGPVDAVFNAIHKIVPHSAALRLFQVHAVTEGTDAQAQVSV 474
                                       .*********99876.679********************************************************** PP

                         TIGR00973 464 vlelngkkysGrgvatdiveasakayvnaln 494
                                       +le +g+ ++G +++td + asakayvnaln
  FitnessBrowser__Caulo:CCNA_01610 475 RLEEDGRIATGAAADTDTLTASAKAYVNALN 505
                                       ******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (524 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: 24.25
//
[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