Alignments for a candidate for leuC in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Caulobacter crescentus NA1000

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate CCNA_00196 CCNA_00196 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Caulo:CCNA_00196
          Length = 479

 Score =  594 bits (1531), Expect = e-174
 Identities = 297/471 (63%), Positives = 359/471 (76%), Gaps = 9/471 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAHVV EA  E  +LYID HL+HEVT+PQAF GLRA GR VR+P +T A  D
Sbjct: 4   KTLYDKIWDAHVVSEAGGEA-ILYIDLHLIHEVTTPQAFAGLRAAGRKVRRPDRTLAVAD 62

Query: 63  HNVSTQTKDINA---CGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HN+ T+ + +       E AR+Q++ L +N  + G+E + +     GIVHV+GPEQG T 
Sbjct: 63  HNIPTEGQALGVDAVADEEARLQLKTLARNVADNGIEFFPMGDIRNGIVHVVGPEQGRTQ 122

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL+Q +AK M + V G+  PG+T
Sbjct: 123 PGMTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLRQKKAKNMLVRVDGQLPPGVT 182

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD+ LA+IG+ G+AGGTG+V+EF GEAI  LSMEGRMTLCN+ IE GAKAGLVAPD+ T
Sbjct: 183 GKDVALAVIGEIGTAGGTGYVIEFAGEAIAGLSMEGRMTLCNLTIEGGAKAGLVAPDDKT 242

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F Y++G+  APKG  +D A+++WKT  TDE A FD  V +    + P VTWGT+P  VI 
Sbjct: 243 FAYIQGKPAAPKGAAWDMALSHWKTFFTDEDAVFDRTVVIDGSALVPMVTWGTSPEDVIP 302

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           V  N+PDP SFA P +RA+A +AL YMGLK G P++E  ID+VFIGSCTNSRIED+RAAA
Sbjct: 303 VTGNVPDPESFATPDKRAAAHRALDYMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAA 362

Query: 360 EIAK-----GRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN 414
            + +     GR VAP V+A+VVPGSG VK QAE EGLD IF  AGF+WR PGCSMCLAMN
Sbjct: 363 AVVQEAFLHGRLVAPHVKAMVVPGSGLVKEQAEEEGLDAIFKAAGFDWREPGCSMCLAMN 422

Query: 415 NDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            D+L P ERCASTSNRNFEGRQGR GRTHLVSPAMAAAAA+ GH  D+R +
Sbjct: 423 PDKLAPQERCASTSNRNFEGRQGRAGRTHLVSPAMAAAAAIAGHLVDVRTL 473


Lambda     K      H
   0.317    0.134    0.396 

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: 774
Number of extensions: 33
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: 466
Length of database: 479
Length adjustment: 33
Effective length of query: 433
Effective length of database: 446
Effective search space:   193118
Effective search space used:   193118
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_00196 CCNA_00196 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.1683.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-233  759.5   0.2     7e-233  759.2   0.2    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00196  CCNA_00196 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00196  CCNA_00196 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  759.2   0.2    7e-233    7e-233       2     465 ..       3     472 ..       2     473 .. 0.97

  Alignments for each domain:
  == domain 1  score: 759.2 bits;  conditional E-value: 7e-233
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr...d 71 
                                            ktly+k++dahvv ea +e  +lyid+hl+hevt+pqaf glraagrkvrr+d+tla  dhni+te +    
  lcl|FitnessBrowser__Caulo:CCNA_00196   3 GKTLYDKIWDAHVVSEAGGE-AILYIDLHLIHEVTTPQAFAGLRAAGRKVRRPDRTLAVADHNIPTEGQalgV 74 
                                           59*************99776.699*******************************************995532 PP

                             TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgi 144
                                             + +e+a+lq+k+l +nv + g+++f + + ++givhvvgpe+g t pg+tivcgdsht+thgafgala gi
  lcl|FitnessBrowser__Caulo:CCNA_00196  75 DAVADEEARLQLKTLARNVADNGIEFFPMGDIRNGIVHVVGPEQGRTQPGMTIVCGDSHTSTHGAFGALAHGI 147
                                           246799******************************************************************* PP

                             TIGR00170 145 gtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                           gtsevehvlatqtl+q++ak++ ++v+g+l +g+t kd+ la+ig ig+aggtgyv+efageai  lsme+rm
  lcl|FitnessBrowser__Caulo:CCNA_00196 148 GTSEVEHVLATQTLRQKKAKNMLVRVDGQLPPGVTGKDVALAVIGEIGTAGGTGYVIEFAGEAIAGLSMEGRM 220
                                           ************************************************************************* PP

                             TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtw 290
                                           t+cn++ie gakagl+apd+ tf+y+++++ apkg+ ++ a+++wkt+ tde+a+fd++v+++++ ++p+vtw
  lcl|FitnessBrowser__Caulo:CCNA_00196 221 TLCNLTIEGGAKAGLVAPDDKTFAYIQGKPAAPKGAAWDMALSHWKTFFTDEDAVFDRTVVIDGSALVPMVTW 293
                                           ************************************************************************* PP

                             TIGR00170 291 gtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk 363
                                           gt+p++v++v+++vpdp+s+a p+++a a +al+y+gl++g+++ + ++d+vfigsctnsried+raaa+vv+
  lcl|FitnessBrowser__Caulo:CCNA_00196 294 GTSPEDVIPVTGNVPDPESFATPDKRAAAHRALDYMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAAAVVQ 366
                                           *********************************************************************9974 PP

                             TIGR00170 364 .....gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnr 431
                                                g+ va+ vk a+vvpgsglvk+qae+egld if +agf+wre+gcs+cl+mn+d+l + ercastsnr
  lcl|FitnessBrowser__Caulo:CCNA_00196 367 eaflhGRLVAPHVK-AMVVPGSGLVKEQAEEEGLDAIFKAAGFDWREPGCSMCLAMNPDKLAPQERCASTSNR 438
                                           444449********.********************************************************** PP

                             TIGR00170 432 nfegrqgkgarthlvspamaaaaavagkfvdire 465
                                           nfegrqg+++rthlvspamaaaaa+ag++vd+r 
  lcl|FitnessBrowser__Caulo:CCNA_00196 439 NFEGRQGRAGRTHLVSPAMAAAAAIAGHLVDVRT 472
                                           ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (479 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.34
//
[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