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.14644.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  lcl|FitnessBrowser__Caulo:CCNA_02204  CCNA_02204 ketol-acid reductoiso


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02204  CCNA_02204 ketol-acid reductoisomerase/2-dehydropantoate 2-reductase
   #    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.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 
                                           ++k+ai+GyGsqG+a+alnlrdsg+ nv v+lr ++ + kkAe +G+kv+tv+ea++ adlimiL pDe q +
  lcl|FitnessBrowser__Caulo:CCNA_02204  16 DRKIAIVGYGSQGHAHALNLRDSGIkNVAVALRAGSPTAKKAEGEGLKVMTVAEAAAWADLIMILAPDEHQAA 88 
                                           789*********************967********************************************** PP

                             TIGR00465  75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgea 147
                                            y++ei+ ++++g+allf+HG n++f  i++++ +dv++vAPKgpG++vR ey++g Gvp liAv++++tg+a
  lcl|FitnessBrowser__Caulo:CCNA_02204  89 IYKNEIALNIRDGAALLFAHGLNVHFGLIEPKDTIDVLMVAPKGPGHTVRGEYQKGGGVPCLIAVHHNATGNA 161
                                           ************************************************************************* PP

                             TIGR00465 148 keiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelkl 220
                                            +  layA aiGg+r g++et F+eE+e+DLfGEqavLcGg  +l++a+f+tLveaGy+pe+Ayfe++helkl
  lcl|FitnessBrowser__Caulo:CCNA_02204 162 LDLGLAYASAIGGGRSGIIETNFREECETDLFGEQAVLCGGTVELVRAGFETLVEAGYAPEMAYFECLHELKL 234
                                           ************************************************************************* PP

                             TIGR00465 221 ivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeeark 292
                                           ivdl++e+G+++m  ++sntA++g++ ++ +i++ e+k+em+ +l++iq+G+f ++++le+++g+p+f+++r+
  lcl|FitnessBrowser__Caulo:CCNA_02204 235 IVDLMYEGGIANMNYSISNTAEYGEYVTGpRIITPETKAEMKRVLEDIQSGKFVRDFMLENAVGQPSFKATRR 307
                                           *****************************9******************************************* PP

                             TIGR00465 293 kekeqeiekvGkelralvka 312
                                           +  e++ie+vG +lr ++++
  lcl|FitnessBrowser__Caulo:CCNA_02204 308 RSAEHQIEEVGARLRGMMPW 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: 00:00:00.01
# Mc/sec: 7.73
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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