GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Klebsiella michiganensis M5al

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate BWI76_RS04130 BWI76_RS04130 2-deoxyribose-5-phosphate aldolase

Query= BRENDA::Q7WT44
         (259 letters)



>FitnessBrowser__Koxy:BWI76_RS04130
          Length = 259

 Score =  494 bits (1272), Expect = e-145
 Identities = 251/259 (96%), Positives = 258/259 (99%)

Query: 1   MTDLSASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60
           MTDL+ASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAA+CIYPRFIPIARKTL
Sbjct: 1   MTDLTASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAAVCIYPRFIPIARKTL 60

Query: 61  NAQGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFD 120
           N QGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFD
Sbjct: 61  NEQGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFD 120

Query: 121 LVKACKEACAAANVLLKVIIETGELKEEALIRKASEISIKAGADFIKTSTGKVPVNATPE 180
           LVKACKEACAAANVLLKVIIETGELKE+ALIRKASEI+IKAGADFIKTSTGKVPVNATPE
Sbjct: 121 LVKACKEACAAANVLLKVIIETGELKEDALIRKASEIAIKAGADFIKTSTGKVPVNATPE 180

Query: 181 SARIMLEVIRDMGVQKTVGFKPAGGVRSAEDAQQFLAIADELFGADWADSRHYRFGASSL 240
           SARIMLEVIRDMGVQ++VGFKPAGGVRSAEDAQ+FLAIADELFGADWADSRHYRFGASSL
Sbjct: 181 SARIMLEVIRDMGVQQSVGFKPAGGVRSAEDAQKFLAIADELFGADWADSRHYRFGASSL 240

Query: 241 LASLLKALGHGDGKSASSY 259
           LASLLKALGHGDGKSASSY
Sbjct: 241 LASLLKALGHGDGKSASSY 259


Lambda     K      H
   0.318    0.133    0.374 

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: 328
Number of extensions: 4
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: 259
Length of database: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate BWI76_RS04130 BWI76_RS04130 (2-deoxyribose-5-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

# 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/TIGR00126.hmm
# target sequence database:        /tmp/gapView.23068.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00126  [M=211]
Accession:   TIGR00126
Description: deoC: deoxyribose-phosphate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
    1.7e-88  281.6   1.3      2e-88  281.4   1.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04130  BWI76_RS04130 2-deoxyribose-5-ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04130  BWI76_RS04130 2-deoxyribose-5-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.4   1.3     2e-88     2e-88       2     210 ..      11     232 ..      10     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 281.4 bits;  conditional E-value: 2e-88
                               TIGR00126   2 lakliDhtalkadtteedietlcaeAkky..kfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGas 67 
                                             ++kl+D+t+l++d+t+e++++lc++Ak++  ++aavc++p+++++A+++L+  gt +++i+tv++FP+G++
  lcl|FitnessBrowser__Koxy:BWI76_RS04130  11 ALKLMDLTTLNDDDTNEKVIALCHQAKTPvgNTAAVCIYPRFIPIARKTLNeqGTpDIRIATVTNFPHGND 81 
                                             689**************************99*******************988999*************** PP

                               TIGR00126  68 ttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveaca..kvllKvilEtalLtdeekk. 135
                                             +++++l+E+++ai++GAdEvDvv++++al ++ne+v+++ +ka++eaca  +vllKvi+Et++L++++++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS04130  82 DIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFDLVKACKEACAaaNVLLKVIIETGELKEDALIr 152
                                             ************************************************999*****************988 PP

                               TIGR00126 136 kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.....evgvKasGGvrtaedalalieagaeri 201
                                             kAsei+i+agadf+Ktstg++ ++At+e++r+m +v++d     +vg+K++GGvr aeda++++++++e++
  lcl|FitnessBrowser__Koxy:BWI76_RS04130 153 KASEIAIKAGADFIKTSTGKVPVNATPESARIMLEVIRDmgvqqSVGFKPAGGVRSAEDAQKFLAIADELF 223
                                             **************************************9999999************************** PP

                               TIGR00126 202 gasaavaii 210
                                             ga++a+ ++
  lcl|FitnessBrowser__Koxy:BWI76_RS04130 224 GADWADSRH 232
                                             *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (259 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: 00:00:00.00
# Mc/sec: 9.35
//
[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