Alignments for a candidate for leuB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Caulobacter crescentus NA1000

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate CCNA_00193 CCNA_00193 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__Caulo:CCNA_00193
          Length = 350

 Score =  421 bits (1083), Expect = e-122
 Identities = 220/359 (61%), Positives = 262/359 (72%), Gaps = 13/359 (3%)

Query: 5   SLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEKA 64
           +L LLPGDGIGPE   +VR++     +A      V E L GG++YD HG  ++D   E+A
Sbjct: 3   TLLLLPGDGIGPEVCAQVRRVA----AALTPDLKVDEALYGGASYDTHGTPLTDEVREQA 58

Query: 65  LAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLKPE 124
           LA+DA+L GAVGGPKW   P   RPEAGLL LRK +++FANLRPA C+ ALA ASSLKPE
Sbjct: 59  LASDAVLMGAVGGPKWADAPRHLRPEAGLLNLRKAMDVFANLRPAYCFEALAGASSLKPE 118

Query: 125 LVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELARSR 184
           LV GLDI+ VREL GGVYFG+P+ I DL +GQK+G DTQ+Y T EIER+  VAFELAR R
Sbjct: 119 LVSGLDIMFVRELVGGVYFGQPRGIEDLADGQKKGFDTQVYTTSEIERVGRVAFELARGR 178

Query: 185 DNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVIVT 244
            N+V S EK NVM+SG+LW QV+TE HA +Y DVQLEH+LAD   MQLVR PKQFDVIVT
Sbjct: 179 TNKVHSAEKSNVMESGLLWKQVITELHAREYPDVQLEHILADNCAMQLVRAPKQFDVIVT 238

Query: 245 DNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIANPI 304
           DNLFGD+LSD AAMLTGSLGMLPSA+LGAP      +  +YEP+HGSAPDIAGK +ANP+
Sbjct: 239 DNLFGDILSDAAAMLTGSLGMLPSAALGAPG-----KPGLYEPIHGSAPDIAGKGLANPL 293

Query: 305 AMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDAVLA 363
           A I SF M LR+S    + A  L AA+   LD G RT D+       + T+ MGDAVLA
Sbjct: 294 AAILSFEMALRWSLKQTEAADALLAAVKAALDNGARTRDLGG----SLTTTQMGDAVLA 348


Lambda     K      H
   0.319    0.135    0.387 

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: 480
Number of extensions: 19
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: 370
Length of database: 350
Length adjustment: 29
Effective length of query: 341
Effective length of database: 321
Effective search space:   109461
Effective search space used:   109461
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CCNA_00193 CCNA_00193 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.23579.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-134  433.8   0.0   2.5e-134  433.7   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00193  CCNA_00193 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00193  CCNA_00193 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.7   0.0  2.5e-134  2.5e-134       3     345 ..       5     346 ..       3     350 .] 0.96

  Alignments for each domain:
  == domain 1  score: 433.7 bits;  conditional E-value: 2.5e-134
                             TIGR00169   3 avLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpk 75 
                                            +LpGDgiGpev a+  +v  a+      +l+ +eal GGa+ d++g+Pl++e  +++ ++davL+gavGGpk
  lcl|FitnessBrowser__Caulo:CCNA_00193   5 LLLPGDGIGPEVCAQVRRVAAAL----TPDLKVDEALYGGASYDTHGTPLTDEVREQALASDAVLMGAVGGPK 73 
                                           68************987776666....5678889*************************************** PP

                             TIGR00169  76 WdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereea 148
                                           W + pr+ rPe gLL+lrk +d+fanLrPa  f++L  +s+lk+e+v+g+D++ vreL+gG+YfG+p+++e+ 
  lcl|FitnessBrowser__Caulo:CCNA_00193  74 WADAPRHLRPEAGLLNLRKAMDVFANLRPAYCFEALAGASSLKPELVSGLDIMFVRELVGGVYFGQPRGIEDL 146
                                           **********************************************************************998 PP

                             TIGR00169 149 ee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehlyi 219
                                            + +kk++dt++Yt++eier+ rvafelar r +kv s +k+nv+es+ lW+++++e++  eyPdv+leh++ 
  lcl|FitnessBrowser__Caulo:CCNA_00193 147 ADgQKKGFDTQVYTTSEIERVGRVAFELARGRTNKVHSAEKSNVMESGLLWKQVITELHArEYPDVQLEHILA 219
                                           888******************************************************9988************ PP

                             TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.kglalfepvhgsapdiagkgianp 291
                                           Dn+amqLv++P+q+dv+vt+nlfGDilsD a+++tGslG+LPsa+l+   + +l+ep+hgsapdiagkg+anp
  lcl|FitnessBrowser__Caulo:CCNA_00193 220 DNCAMQLVRAPKQFDVIVTDNLFGDILSDAAAMLTGSLGMLPSAALGApGKPGLYEPIHGSAPDIAGKGLANP 292
                                           ***********************************************945679******************** PP

                             TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345
                                           +aails  + lr sl++ eaa+a+ aavk +l++g rt+dl+++ tt+++ ++v
  lcl|FitnessBrowser__Caulo:CCNA_00193 293 LAAILSFEMALRWSLKQTEAADALLAAVKAALDNGARTRDLGGSLTTTQMGDAV 346
                                           ******************************************999888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (350 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.04
//
[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