Alignments for a candidate for glpK in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Caulobacter crescentus NA1000

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate CCNA_01281 CCNA_01281 glycerol kinase

Query= reanno::Smeli:SM_b21009
         (497 letters)



>FitnessBrowser__Caulo:CCNA_01281
          Length = 496

 Score =  498 bits (1283), Expect = e-145
 Identities = 260/489 (53%), Positives = 318/489 (65%), Gaps = 2/489 (0%)

Query: 5   ILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVKEAIE 64
           ILA+DQGTTSTRAI+FD      G   +  +Q +P  GWVEHD EEI+   V+ ++E  E
Sbjct: 6   ILALDQGTTSTRAILFDRAGTALGDASRPLRQSYPADGWVEHDAEEIYAAAVAVLREVTE 65

Query: 65  KSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLEKTFV 124
            SG  A DIAAIG+TNQRETVVVWDR TG+PIH AIVWQDRRTA  C +LK +G E    
Sbjct: 66  ASGRMA-DIAAIGVTNQRETVVVWDRATGRPIHPAIVWQDRRTADVCARLKAEGHEPRVT 124

Query: 125 KKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCTDATN 184
           + TGLLLDPYFS TK+ W+L    GA+ RA  GEL  GT+D ++IWRLTGG    TDATN
Sbjct: 125 EVTGLLLDPYFSATKIAWILDKTPGARARAEAGELLCGTMDCWVIWRLTGGAVHATDATN 184

Query: 185 ASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGVAGDQ 244
           ASRTLL++I   AW  E+  +  VP  +LP+V DC  D+G T   + G  +PI GVAGDQ
Sbjct: 185 ASRTLLFDIGAQAWSSEMLALFNVPSTILPKVLDCVDDYGATQADILGREVPIRGVAGDQ 244

Query: 245 QAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYALEGSI 304
           QAA +GQ C  PG +K+TYGTGCF L+NTG D   S+ RLLTT+A R+ G+TTYALEGSI
Sbjct: 245 QAALMGQGCVAPGQMKATYGTGCFMLINTGTDRAVSRARLLTTVAARVGGKTTYALEGSI 304

Query: 305 FVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARGAIFG 364
           FVAGAA+QWL +GL +        +LA +A P   V +VPAFTGLGAP WD +ARG IFG
Sbjct: 305 FVAGAAIQWLGEGLGITGGPRAAEALARAAKPDHAVVVVPAFTGLGAPWWDAEARGGIFG 364

Query: 365 MTRNTGPAEFARAALEAVCYQTRDLLEAMHKDW-RRNGNDTVLRVDGGMVASDWTMQRLS 423
           +TR+ G  E A A  +A   Q+RDL+EAM  D     G    LR+DGGM  S W  QRL+
Sbjct: 365 LTRDAGLPEIAAATFDACALQSRDLIEAMRADAPTAFGEAAQLRIDGGMAKSAWFSQRLA 424

Query: 424 DLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRKVKL 483
           DL    V R    ETTALG A  A   AG++ + E  A++        P MD+  R+   
Sbjct: 425 DLTGLSVRRASYQETTALGAALFAAVGAGLYGSIEEAAEASPAAETLAPAMDDHVREAAY 484

Query: 484 KGWRSAVKR 492
             W  AV R
Sbjct: 485 ARWLDAVPR 493


Lambda     K      H
   0.319    0.134    0.415 

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: 755
Number of extensions: 32
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: 497
Length of database: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_01281 CCNA_01281 (glycerol kinase)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

# 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.carbon/TIGR01311.hmm
# target sequence database:        /tmp/gapView.21491.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01311  [M=496]
Accession:   TIGR01311
Description: glycerol_kin: glycerol kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-201  654.6   0.1   4.4e-201  654.4   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01281  CCNA_01281 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01281  CCNA_01281 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  654.4   0.1  4.4e-201  4.4e-201       2     493 ..       5     494 ..       4     496 .] 0.98

  Alignments for each domain:
  == domain 1  score: 654.4 bits;  conditional E-value: 4.4e-201
                             TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                           li+a+DqGtts+rai+fd+ g+ ++ a++ l+q++p +gwvEhd++ei++++v+vl+e++e+++ ++++iaai
  lcl|FitnessBrowser__Caulo:CCNA_01281   5 LILALDQGTTSTRAILFDRAGTALGDASRPLRQSYPADGWVEHDAEEIYAAAVAVLREVTEASG-RMADIAAI 76 
                                           89********************************************************998766.899***** PP

                             TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147
                                           G+tnqREt+vvWd++tg+p+++aivWqd+rta+++++lk+e++e +++e tGL+l++YfsatK++W+ld++++
  lcl|FitnessBrowser__Caulo:CCNA_01281  77 GVTNQRETVVVWDRATGRPIHPAIVWQDRRTADVCARLKAEGHEPRVTEVTGLLLDPYFSATKIAWILDKTPG 149
                                           ************************************************************************* PP

                             TIGR01311 148 vrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220
                                           +r++ae+gell+Gt+d+w+i++Ltgg+vh+td+tNASRtll+++  ++w++e+l+lf++p+++lP++ ++ + 
  lcl|FitnessBrowser__Caulo:CCNA_01281 150 ARARAEAGELLCGTMDCWVIWRLTGGAVHATDATNASRTLLFDIGAQAWSSEMLALFNVPSTILPKVLDCVDD 222
                                           ************************************************************************* PP

                             TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklgg 293
                                           yg ++++ +l++evpi+gv+Gdqqaal+gq c+++g++K+tYgtGcF+l+ntG++ ++s+ +lLttva ++gg
  lcl|FitnessBrowser__Caulo:CCNA_01281 223 YGATQAD-ILGREVPIRGVAGDQQAALMGQGCVAPGQMKATYGTGCFMLINTGTDRAVSRARLLTTVAARVGG 294
                                           *****99.***************************************************************** PP

                             TIGR01311 294 kkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGl 366
                                           k++  yalEGs++vaGaa+qwl + l++    +++e+la++++ ++ v++VPaf+GL+aP+Wd++Arg i+Gl
  lcl|FitnessBrowser__Caulo:CCNA_01281 295 KTT--YALEGSIFVAGAAIQWLGEGLGITGGPRAAEALARAAKPDHAVVVVPAFTGLGAPWWDAEARGGIFGL 365
                                           996..******************************************************************** PP

                             TIGR01311 367 trkttkehiaraaleavafqardileamekdag...vevkvLkvDGglsknnllmqiqadilgvkverpkvae 436
                                           tr++   +ia a+++a+a+q+rd++eam++da     e ++L++DGg++k+ ++ q  ad+ g++v+r++++e
  lcl|FitnessBrowser__Caulo:CCNA_01281 366 TRDAGLPEIAAATFDACALQSRDLIEAMRADAPtafGEAAQLRIDGGMAKSAWFSQRLADLTGLSVRRASYQE 438
                                           *******************************995556777********************************* PP

                             TIGR01311 437 ttalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeavers 493
                                           ttalGaAl+a++ +g++ s ee+++ + a+ +t++p+md++ re+ y++w +av r 
  lcl|FitnessBrowser__Caulo:CCNA_01281 439 TTALGAALFAAVGAGLYGSIEEAAEASPAA-ETLAPAMDDHVREAAYARWLDAVPRV 494
                                           **********************99999886.9**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (496 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 12.01
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources