GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Klebsiella michiganensis M5al

Align Deoxyribose-phosphate aldolase; DERA; EC 4.1.2.4; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase (uncharacterized)
to candidate BWI76_RS23665 BWI76_RS23665 2-deoxyribose-5-phosphate aldolase

Query= curated2:A6T962
         (249 letters)



>FitnessBrowser__Koxy:BWI76_RS23665
          Length = 249

 Score =  476 bits (1224), Expect = e-139
 Identities = 238/249 (95%), Positives = 243/249 (97%)

Query: 1   MKAIKNKGQDKTMNETTHRFARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWT 60
           MK IKNK QD+TMNETT RFARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWT
Sbjct: 1   MKVIKNKEQDETMNETTRRFARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWT 60

Query: 61  RFLSTLLPQQGTGEVMIGGPVGFPGGGHTTDTKVQEVRQLIADGAREVDMVVNIGKVLSG 120
           RFLSTLLPQQGTGEVMIGGPVGFPGGGH TDTKVQEVRQLIADGAREVDMVVNIGKVLSG
Sbjct: 61  RFLSTLLPQQGTGEVMIGGPVGFPGGGHATDTKVQEVRQLIADGAREVDMVVNIGKVLSG 120

Query: 121 DYDYVREDLRRVVEAAAPVPAKVILETHYLNEEQIRRVCEIAVEVGMKWVKTSTGWAPTG 180
           DYDYVREDLRRVV+AAAPVPAKVILETHYLNEEQIRRVC+IAVEVGMKWVKTSTGWAPTG
Sbjct: 121 DYDYVREDLRRVVDAAAPVPAKVILETHYLNEEQIRRVCDIAVEVGMKWVKTSTGWAPTG 180

Query: 181 ATVEKVRIIADQLKGRIDIKGAGGIRDLATVRALYQLGVRRFGMSHGAVTKVLAELEQHP 240
           ATVEKV IIADQLKGRIDIKGAGGIRDLATVRALYQLG+RRFGMSHGAV+KVL ELEQHP
Sbjct: 181 ATVEKVSIIADQLKGRIDIKGAGGIRDLATVRALYQLGIRRFGMSHGAVSKVLTELEQHP 240

Query: 241 ERFPELNAD 249
           ERFPELNAD
Sbjct: 241 ERFPELNAD 249


Lambda     K      H
   0.319    0.135    0.393 

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: 298
Number of extensions: 5
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: 249
Length of database: 249
Length adjustment: 24
Effective length of query: 225
Effective length of database: 225
Effective search space:    50625
Effective search space used:    50625
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: 46 (22.3 bits)

Align candidate BWI76_RS23665 BWI76_RS23665 (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.17402.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
    3.4e-57  179.3   0.0    4.4e-57  178.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23665  BWI76_RS23665 2-deoxyribose-5-ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23665  BWI76_RS23665 2-deoxyribose-5-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.9   0.0   4.4e-57   4.4e-57       2     207 ..      20     228 ..      19     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.9 bits;  conditional E-value: 4.4e-57
                               TIGR00126   2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGastt 69 
                                             +a+l+D++a++a +te+d+ ++ + A +y++++v v p + ++   lL   gt ev i   vgFP G + t
  lcl|FitnessBrowser__Koxy:BWI76_RS23665  20 FARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWTRFLSTLLPqqGTgEVMIGGPVGFPGGGHAT 90 
                                             689********************************************9767999***************** PP

                               TIGR00126  70 evkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekkkAsei 140
                                             ++k+ E ++ i+ GA EvD+v+ni+++ +++ + v ed++ vv+a+a v+ KvilEt +L +e++++ ++i
  lcl|FitnessBrowser__Koxy:BWI76_RS23665  91 DTKVQEVRQLIADGAREVDMVVNIGKVLSGDYDYVREDLRRVVDAAAPVPAKVILETHYLNEEQIRRVCDI 161
                                             *********************************************************************** PP

                               TIGR00126 141 sieagadfvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaav 207
                                             ++e g ++vKtstg++ +gAtve v ++ +  ++++ +K +GG+r+  ++ al + g  r+g s++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS23665 162 AVEVGMKWVKTSTGWAPTGATVEKVSIIADQLKGRIDIKGAGGIRDLATVRALYQLGIRRFGMSHGA 228
                                             ***************************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (249 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: 9.28
//
[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