Alignments for a candidate for iolC in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Caulobacter crescentus NA1000

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate CCNA_01356 CCNA_01356 5-dehydro-2-deoxygluconokinase IolC

Query= reanno::Caulo:CCNA_01356
         (642 letters)



>FitnessBrowser__Caulo:CCNA_01356
          Length = 642

 Score = 1283 bits (3320), Expect = 0.0
 Identities = 642/642 (100%), Positives = 642/642 (100%)

Query: 1   MAQDAKTLDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLL 60
           MAQDAKTLDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLL
Sbjct: 1   MAQDAKTLDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLL 60

Query: 61  TRVGADHMGRFIREQLEREGVDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMA 120
           TRVGADHMGRFIREQLEREGVDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMA
Sbjct: 61  TRVGADHMGRFIREQLEREGVDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMA 120

Query: 121 LEPSDVDEAWFAQAGAVLINGTHLSQPNVYETSLKAARAVKAAGGRVAFDIDYRPVLWGL 180
           LEPSDVDEAWFAQAGAVLINGTHLSQPNVYETSLKAARAVKAAGGRVAFDIDYRPVLWGL
Sbjct: 121 LEPSDVDEAWFAQAGAVLINGTHLSQPNVYETSLKAARAVKAAGGRVAFDIDYRPVLWGL 180

Query: 181 TGKDAGENRFVENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDTIAALRAIRRASDAL 240
           TGKDAGENRFVENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDTIAALRAIRRASDAL
Sbjct: 181 TGKDAGENRFVENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDTIAALRAIRRASDAL 240

Query: 241 LVCKRGPEGCVAFPGAIPDALDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVET 300
           LVCKRGPEGCVAFPGAIPDALDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVET
Sbjct: 241 LVCKRGPEGCVAFPGAIPDALDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVET 300

Query: 301 CCEWGNACGAIVVSRHGCTPAMPTWIELQAFLSERERPFRLREDAELEHIHWATTRERVY 360
           CCEWGNACGAIVVSRHGCTPAMPTWIELQAFLSERERPFRLREDAELEHIHWATTRERVY
Sbjct: 301 CCEWGNACGAIVVSRHGCTPAMPTWIELQAFLSERERPFRLREDAELEHIHWATTRERVY 360

Query: 361 DELTVLAIDHRSQFEDLIAETGGDAERIPDFKRLALRAVQMVAGRDETRFGMLLDGRFGF 420
           DELTVLAIDHRSQFEDLIAETGGDAERIPDFKRLALRAVQMVAGRDETRFGMLLDGRFGF
Sbjct: 361 DELTVLAIDHRSQFEDLIAETGGDAERIPDFKRLALRAVQMVAGRDETRFGMLLDGRFGF 420

Query: 421 EALAEAADHDYWIARPIELPKSRPLEFECSADVATELLEWPLNQVVKCLAFYHPDDESDL 480
           EALAEAADHDYWIARPIELPKSRPLEFECSADVATELLEWPLNQVVKCLAFYHPDDESDL
Sbjct: 421 EALAEAADHDYWIARPIELPKSRPLEFECSADVATELLEWPLNQVVKCLAFYHPDDESDL 480

Query: 481 RERQERQLLRLADACRKTRHELLLELILPRGMSSDSRTVARAIRRLYALGIRPDWWKLEP 540
           RERQERQLLRLADACRKTRHELLLELILPRGMSSDSRTVARAIRRLYALGIRPDWWKLEP
Sbjct: 481 RERQERQLLRLADACRKTRHELLLELILPRGMSSDSRTVARAIRRLYALGIRPDWWKLEP 540

Query: 541 LTDPDAWREIEIAIAENDPLCRGVVLLGLSAPEAELVASFEVVAPFPIVKGFAVGRTIFY 600
           LTDPDAWREIEIAIAENDPLCRGVVLLGLSAPEAELVASFEVVAPFPIVKGFAVGRTIFY
Sbjct: 541 LTDPDAWREIEIAIAENDPLCRGVVLLGLSAPEAELVASFEVVAPFPIVKGFAVGRTIFY 600

Query: 601 DVARAWLSNQIDDDAAVTALAAKFKVLVDAWRRLRGSVEKAA 642
           DVARAWLSNQIDDDAAVTALAAKFKVLVDAWRRLRGSVEKAA
Sbjct: 601 DVARAWLSNQIDDDAAVTALAAKFKVLVDAWRRLRGSVEKAA 642


Lambda     K      H
   0.322    0.138    0.419 

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: 1512
Number of extensions: 38
Number of successful extensions: 1
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: 642
Length of database: 642
Length adjustment: 38
Effective length of query: 604
Effective length of database: 604
Effective search space:   364816
Effective search space used:   364816
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate CCNA_01356 CCNA_01356 (5-dehydro-2-deoxygluconokinase IolC)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))

# 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/TIGR04382.hmm
# target sequence database:        /tmp/gapView.4370.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04382  [M=309]
Accession:   TIGR04382
Description: myo_inos_iolC_N: 5-dehydro-2-deoxygluconokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-128  414.7   0.1   3.7e-128  413.1   0.0    1.7  2  lcl|FitnessBrowser__Caulo:CCNA_01356  CCNA_01356 5-dehydro-2-deoxygluc


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01356  CCNA_01356 5-dehydro-2-deoxygluconokinase IolC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.1   0.0  3.7e-128  3.7e-128       2     309 .]       8     332 ..       7     332 .. 0.99
   2 ?   -1.3   0.0     0.053     0.053     149     194 ..     352     404 ..     344     413 .. 0.70

  Alignments for each domain:
  == domain 1  score: 413.1 bits;  conditional E-value: 3.7e-128
                             TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 
                                           ldli++GR++vDly+qq+g +led+ sfakylGGsp+N+a+g arlGlkt+l+t+vg+d++Grf+re+lereg
  lcl|FitnessBrowser__Caulo:CCNA_01356   8 LDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLLTRVGADHMGRFIREQLEREG 80 
                                           8************************************************************************ PP

                             TIGR04382  75 vdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreav 147
                                           vd+++v +d++++t+lv+l+i+d+ +fpl+fYRen+aD+al+++dvde+++a+a a+l++gt+ls++++ e++
  lcl|FitnessBrowser__Caulo:CCNA_01356  81 VDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMALEPSDVDEAWFAQAGAVLINGTHLSQPNVYETS 153
                                           ************************************************************************* PP

                             TIGR04382 148 lkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEfeiaagekdd 208
                                           lka+++ k+ag +v++DiDYRpvlW+            ++++++a+lq+v++++d+i+GteeE++i+ g++d+
  lcl|FitnessBrowser__Caulo:CCNA_01356 154 LKAARAVKAAGGRVAFDIDYRPVLWGltgkdagenrfvENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDT 226
                                           ************************************************************************* PP

                             TIGR04382 209 eaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasgllygllegedle 276
                                            aa++a+++++++l+v+KrG+eG++++ ++     +e v+++gfkvev++vlGaGDaF++g+l+g+l++e++e
  lcl|FitnessBrowser__Caulo:CCNA_01356 227 IAALRAIRRASDALLVCKRGPEGCVAFPGAipdalDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVE 299
                                           *****************************9999**************************************** PP

                             TIGR04382 277 kalelanAagaivvsrlscaeamptleeleefl 309
                                           +++e++nA+gaivvsr++c++ampt+ el++fl
  lcl|FitnessBrowser__Caulo:CCNA_01356 300 TCCEWGNACGAIVVSRHGCTPAMPTWIELQAFL 332
                                           ******************************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.053
                             TIGR04382 149 kalelakkagvkvvlDiDYRpvlWk.......skeeasaalqlvlkkvdviiG 194
                                            a ++ + ++  +vl iD+R+++ +       ++e++    +l+l+ v+++ G
  lcl|FitnessBrowser__Caulo:CCNA_01356 352 WATTRERVYDELTVLAIDHRSQFEDliaetggDAERIPDFKRLALRAVQMVAG 404
                                           566778888999********987666666665555565556666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (642 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: 11.16
//
[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