Alignments for a candidate for iolC in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Dinoroseobacter shibae DFL-12

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92) (characterized)
to candidate 3607860 Dshi_1268 PfkB domain protein (RefSeq)

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



>FitnessBrowser__Dino:3607860
          Length = 333

 Score =  514 bits (1324), Expect = e-150
 Identities = 255/316 (80%), Positives = 282/316 (89%)

Query: 11  LAGRNFLVIGRVGMDLCPTPAGTATADAQDMMVAMGGSSANIAAGLVKMGCRSALVTSVS 70
           +  RNFLVIGRVGMDL P PAGTA  DA D+MVAMGGSSANIAAGLVK G R+ALVT VS
Sbjct: 8   IRSRNFLVIGRVGMDLSPAPAGTAIEDATDLMVAMGGSSANIAAGLVKFGARAALVTRVS 67

Query: 71  DDAVGWYCLNQLDHYGVDRTHVKRITGEYRTSLAVYESRVEDHQSVIYRNNAADFQMTIA 130
           DDAVG YCLNQL  YGVD THV  + GE+R SLA+YESR+ DH SVIYRN AADFQM++A
Sbjct: 68  DDAVGRYCLNQLAAYGVDATHVTPVAGEFRNSLALYESRLADHNSVIYRNGAADFQMSVA 127

Query: 131 DVEAVDYSQYSALITAGTVFAAEPSRSATFRAFDLARAAGLPIIFDVDYRPYSWPSPEVA 190
           DVEAVDYSQY ALITAGTVFAAEPSRSATFRAF+LARAAGLPIIFDVDYRPYSWPSP+VA
Sbjct: 128 DVEAVDYSQYGALITAGTVFAAEPSRSATFRAFELARAAGLPIIFDVDYRPYSWPSPQVA 187

Query: 191 ADVLSRAGAMSDIIVGNDEEFGFMAGGIDKGRAKARALAETSASVVVYKMGPKGAVTFAD 250
            +VLSRAGA+SDIIV NDEEFGFMAGGIDKG AKAR LA+TSA +VVYKMGP+GA+TFA+
Sbjct: 188 EEVLSRAGALSDIIVANDEEFGFMAGGIDKGLAKARELAQTSAGIVVYKMGPEGAITFAN 247

Query: 251 GQEIRTGIYPVDALKPTGAGDSFMAGFLASLSEGRPMKDAILRGSACASVVVAKPGCAPA 310
           G E+RTGIYPV ALKPTGAGDSFMAGFLASL+EGR +++A+LRGSACA++VVAKPGCAPA
Sbjct: 248 GTELRTGIYPVTALKPTGAGDSFMAGFLASLAEGRELREAVLRGSACAAIVVAKPGCAPA 307

Query: 311 MPDLAALEAFLATHPG 326
           MPD   L+AFLA HPG
Sbjct: 308 MPDARELDAFLARHPG 323


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: 441
Number of extensions: 15
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: 333
Length adjustment: 28
Effective length of query: 302
Effective length of database: 305
Effective search space:    92110
Effective search space used:    92110
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 3607860 Dshi_1268 (PfkB domain protein (RefSeq))
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.7299.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.5e-105  337.3   0.2   5.1e-105  337.1   0.2    1.0  1  lcl|FitnessBrowser__Dino:3607860  Dshi_1268 PfkB domain protein (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607860  Dshi_1268 PfkB domain protein (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.1   0.2  5.1e-105  5.1e-105       3     309 .]      12     318 ..      10     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 337.1 bits;  conditional E-value: 5.1e-105
                         TIGR04382   3 dlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreeleregvdtsh 79 
                                       ++++iGRvg+Dl ++ +g+++ed+++ +  +GGs+aNia+g+ ++G+++al+t+v+dd++Gr+++++l++ gvd++h
  lcl|FitnessBrowser__Dino:3607860  12 NFLVIGRVGMDLSPAPAGTAIEDATDLMVAMGGSSANIAAGLVKFGARAALVTRVSDDAVGRYCLNQLAAYGVDATH 88 
                                       789************************************************************************** PP

                         TIGR04382  80 vvtdk.eartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreavlkalelak 155
                                       v+  + e+r+sl+l+e + +d ++ ++YR+ aaD++++v+dv++  ++++ al+++gt +++epsr+a+++a+ela+
  lcl|FitnessBrowser__Dino:3607860  89 VTPVAgEFRNSLALYESRLAD-HNSVIYRNGAADFQMSVADVEAVDYSQYGALITAGTVFAAEPSRSATFRAFELAR 164
                                       *****99************99.999**************************************************** PP

                         TIGR04382 156 kagvkvvlDiDYRpvlWkskeeasaalqlvlkkvdviiGteeEfeiaag.ekddeaaakallelgaelvvvKrGeeG 231
                                       +ag  +++D+DYRp++W s++ a+++l+++ +++d+i++++eEf ++ag  ++  a+a++l++++a +vv+K+G+eG
  lcl|FitnessBrowser__Dino:3607860 165 AAGLPIIFDVDYRPYSWPSPQVAEEVLSRAGALSDIIVANDEEFGFMAGgIDKGLAKARELAQTSAGIVVYKMGPEG 241
                                       ***********************************************88689999********************** PP

                         TIGR04382 232 slvytkdeeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsrlscaeamptleeleef 308
                                       ++++++  +e+++++++v++lk  GaGD+F++g+l +l eg++l++a+  ++A++aivv++ +ca+amp+++el++f
  lcl|FitnessBrowser__Dino:3607860 242 AITFANG-TELRTGIYPVTALKPTGAGDSFMAGFLASLAEGRELREAVLRGSACAAIVVAKPGCAPAMPDARELDAF 317
                                       *****99.*******************************************************************99 PP

                         TIGR04382 309 l 309
                                       l
  lcl|FitnessBrowser__Dino:3607860 318 L 318
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (333 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: 8.51
//
[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