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.18473.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: 7.83
//
[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:

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:

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:

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:

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