Alignments for a candidate for ilvC in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Caulobacter crescentus NA1000

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate CCNA_02204 CCNA_02204 ketol-acid reductoisomerase/2-dehydropantoate 2-reductase

Query= metacyc::MONOMER-18814
         (338 letters)



>FitnessBrowser__Caulo:CCNA_02204
          Length = 339

 Score =  476 bits (1226), Expect = e-139
 Identities = 231/339 (68%), Positives = 277/339 (81%), Gaps = 1/339 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59
           M+V+YD+DADL+ I  + + I+GYGSQGHAHALNL+DSG+ NV V LR    +  KA   
Sbjct: 1   MRVYYDRDADLARILDRKIAIVGYGSQGHAHALNLRDSGIKNVAVALRAGSPTAKKAEGE 60

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           GL+V  VAEA   AD++MIL PDE  A +YKNE+  NI++GAAL FAHG NVH+G + P+
Sbjct: 61  GLKVMTVAEAAAWADLIMILAPDEHQAAIYKNEIALNIRDGAALLFAHGLNVHFGLIEPK 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
             +DV+M+APK PGHTVR  Y +GGGVP LIAVH N +G A D+ L+YA+A GGGR+GII
Sbjct: 121 DTIDVLMVAPKGPGHTVRGEYQKGGGVPCLIAVHHNATGNALDLGLAYASAIGGGRSGII 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ETNFREE ETDLFGEQAVLCGGTVEL++AGFETLVEAGYAPEMAYFECLHELKLIVDL+Y
Sbjct: 181 ETNFREECETDLFGEQAVLCGGTVELVRAGFETLVEAGYAPEMAYFECLHELKLIVDLMY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299
           EGGIANMNYSISN AEYGEYVTGPR++T ETK  MK+ L DIQ+G++ + F+LEN  G P
Sbjct: 241 EGGIANMNYSISNTAEYGEYVTGPRIITPETKAEMKRVLEDIQSGKFVRDFMLENAVGQP 300

Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           +  + RR +AEHQIEEVGA+LR MMPWIAKNK+VDQ+KN
Sbjct: 301 SFKATRRRSAEHQIEEVGARLRGMMPWIAKNKLVDQAKN 339


Lambda     K      H
   0.316    0.133    0.379 

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: 427
Number of extensions: 15
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: 338
Length of database: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate CCNA_02204 CCNA_02204 (ketol-acid reductoisomerase/2-dehydropantoate 2-reductase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.640258.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.3e-131  422.5   0.2   5.1e-131  422.3   0.2    1.0  1  FitnessBrowser__Caulo:CCNA_02204  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_02204  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.3   0.2  5.1e-131  5.1e-131       3     312 ..      16     327 ..      14     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 422.3 bits;  conditional E-value: 5.1e-131
                         TIGR00465   3 gkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkevyea 78 
                                       ++k+ai+GyGsqG+a+alnlrdsg+ nv v+lr ++ + kkAe +G+kv+tv+ea++ adlimiL pDe q + y++
  FitnessBrowser__Caulo:CCNA_02204  16 DRKIAIVGYGSQGHAHALNLRDSGIkNVAVALRAGSPTAKKAEGEGLKVMTVAEAAAWADLIMILAPDEHQAAIYKN 92 
                                       789*********************967************************************************** PP

                         TIGR00465  79 eikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAlayA 155
                                       ei+ ++++g+allf+HG n++f  i++++ +dv++vAPKgpG++vR ey++g Gvp liAv++++tg+a +  layA
  FitnessBrowser__Caulo:CCNA_02204  93 EIALNIRDGAALLFAHGLNVHFGLIEPKDTIDVLMVAPKGPGHTVRGEYQKGGGVPCLIAVHHNATGNALDLGLAYA 169
                                       ***************************************************************************** PP

                         TIGR00465 156 kaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlel 232
                                        aiGg+r g++et F+eE+e+DLfGEqavLcGg  +l++a+f+tLveaGy+pe+Ayfe++helklivdl++e+G+++
  FitnessBrowser__Caulo:CCNA_02204 170 SAIGGGRSGIIETNFREECETDLFGEQAVLCGGTVELVRAGFETLVEAGYAPEMAYFECLHELKLIVDLMYEGGIAN 246
                                       ***************************************************************************** PP

                         TIGR00465 233 mrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelra 308
                                       m  ++sntA++g++ ++ +i++ e+k+em+ +l++iq+G+f ++++le+++g+p+f+++r++  e++ie+vG +lr 
  FitnessBrowser__Caulo:CCNA_02204 247 MNYSISNTAEYGEYVTGpRIITPETKAEMKRVLEDIQSGKFVRDFMLENAVGQPSFKATRRRSAEHQIEEVGARLRG 323
                                       *****************9*********************************************************** PP

                         TIGR00465 309 lvka 312
                                       ++++
  FitnessBrowser__Caulo:CCNA_02204 324 MMPW 327
                                       **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (339 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: 00:00:00.00
# Mc/sec: 19.75
//
[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