Alignments for a candidate for iolC in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Phaeobacter inhibens BS107

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92) (characterized)
to candidate GFF709 PGA1_c07240 putative 5-dehydro-2-deoxygluconokinase

Query= reanno::Phaeo:GFF709
         (330 letters)



>FitnessBrowser__Phaeo:GFF709
          Length = 330

 Score =  652 bits (1681), Expect = 0.0
 Identities = 330/330 (100%), Positives = 330/330 (100%)

Query: 1   MGQPSKARSDLAGRNFLVIGRVGMDLCPTPAGTATADAQDMMVAMGGSSANIAAGLVKMG 60
           MGQPSKARSDLAGRNFLVIGRVGMDLCPTPAGTATADAQDMMVAMGGSSANIAAGLVKMG
Sbjct: 1   MGQPSKARSDLAGRNFLVIGRVGMDLCPTPAGTATADAQDMMVAMGGSSANIAAGLVKMG 60

Query: 61  CRSALVTSVSDDAVGWYCLNQLDHYGVDRTHVKRITGEYRTSLAVYESRVEDHQSVIYRN 120
           CRSALVTSVSDDAVGWYCLNQLDHYGVDRTHVKRITGEYRTSLAVYESRVEDHQSVIYRN
Sbjct: 61  CRSALVTSVSDDAVGWYCLNQLDHYGVDRTHVKRITGEYRTSLAVYESRVEDHQSVIYRN 120

Query: 121 NAADFQMTIADVEAVDYSQYSALITAGTVFAAEPSRSATFRAFDLARAAGLPIIFDVDYR 180
           NAADFQMTIADVEAVDYSQYSALITAGTVFAAEPSRSATFRAFDLARAAGLPIIFDVDYR
Sbjct: 121 NAADFQMTIADVEAVDYSQYSALITAGTVFAAEPSRSATFRAFDLARAAGLPIIFDVDYR 180

Query: 181 PYSWPSPEVAADVLSRAGAMSDIIVGNDEEFGFMAGGIDKGRAKARALAETSASVVVYKM 240
           PYSWPSPEVAADVLSRAGAMSDIIVGNDEEFGFMAGGIDKGRAKARALAETSASVVVYKM
Sbjct: 181 PYSWPSPEVAADVLSRAGAMSDIIVGNDEEFGFMAGGIDKGRAKARALAETSASVVVYKM 240

Query: 241 GPKGAVTFADGQEIRTGIYPVDALKPTGAGDSFMAGFLASLSEGRPMKDAILRGSACASV 300
           GPKGAVTFADGQEIRTGIYPVDALKPTGAGDSFMAGFLASLSEGRPMKDAILRGSACASV
Sbjct: 241 GPKGAVTFADGQEIRTGIYPVDALKPTGAGDSFMAGFLASLSEGRPMKDAILRGSACASV 300

Query: 301 VVAKPGCAPAMPDLAALEAFLATHPGATEL 330
           VVAKPGCAPAMPDLAALEAFLATHPGATEL
Sbjct: 301 VVAKPGCAPAMPDLAALEAFLATHPGATEL 330


Lambda     K      H
   0.319    0.132    0.386 

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: 524
Number of extensions: 11
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: 330
Length of database: 330
Length adjustment: 28
Effective length of query: 302
Effective length of database: 302
Effective search space:    91204
Effective search space used:    91204
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: 49 (23.5 bits)

Align candidate GFF709 PGA1_c07240 (putative 5-dehydro-2-deoxygluconokinase)
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.2397.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     7e-102  326.8   0.4   7.9e-102  326.6   0.4    1.0  1  lcl|FitnessBrowser__Phaeo:GFF709  PGA1_c07240 putative 5-dehydro-2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF709  PGA1_c07240 putative 5-dehydro-2-deoxygluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.6   0.4  7.9e-102  7.9e-102       3     309 .]      15     321 ..      13     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 326.6 bits;  conditional E-value: 7.9e-102
                         TIGR04382   3 dlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreeleregvdtsh 79 
                                       ++++iGRvg+Dl ++ +g++ +d+++ +  +GGs+aNia+g+ ++G ++al+t v+dd++G +++++l + gvd +h
  lcl|FitnessBrowser__Phaeo:GFF709  15 NFLVIGRVGMDLCPTPAGTATADAQDMMVAMGGSSANIAAGLVKMGCRSALVTSVSDDAVGWYCLNQLDHYGVDRTH 91 
                                       789************************************************************************** PP

                         TIGR04382  80 vvtdk.eartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreavlkalelak 155
                                       v++   e+rtsl+++e + +d ++ ++YR+naaD+++t++dv++  +++++al+++gt +++epsr+a+++a++la+
  lcl|FitnessBrowser__Phaeo:GFF709  92 VKRITgEYRTSLAVYESRVED-HQSVIYRNNAADFQMTIADVEAVDYSQYSALITAGTVFAAEPSRSATFRAFDLAR 167
                                       *****99***********999.9999*************************************************** PP

                         TIGR04382 156 kagvkvvlDiDYRpvlWkskeeasaalqlvlkkvdviiGteeEfeiaag.ekddeaaakallelgaelvvvKrGeeG 231
                                       +ag  +++D+DYRp++W s+e a+ +l+++ +++d+i+G++eEf ++ag  ++ +a+a+al+e++a++vv+K+G++G
  lcl|FitnessBrowser__Phaeo:GFF709 168 AAGLPIIFDVDYRPYSWPSPEVAADVLSRAGAMSDIIVGNDEEFGFMAGgIDKGRAKARALAETSASVVVYKMGPKG 244
                                       ***********************************************886899999********************* PP

                         TIGR04382 232 slvytkdeeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsrlscaeamptleeleef 308
                                       ++++++  +e+++++++v++lk  GaGD+F++g+l +l eg+++++a+  ++A++++vv++ +ca+amp+l+ le+f
  lcl|FitnessBrowser__Phaeo:GFF709 245 AVTFADG-QEIRTGIYPVDALKPTGAGDSFMAGFLASLSEGRPMKDAILRGSACASVVVAKPGCAPAMPDLAALEAF 320
                                       ****998.9******************************************************************99 PP

                         TIGR04382 309 l 309
                                       l
  lcl|FitnessBrowser__Phaeo:GFF709 321 L 321
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (330 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: 8.52
//
[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