GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmB in Pedobacter sp. GW460-11-11-14-LB5

Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate CA265_RS24650 CA265_RS24650 beta-phosphoglucomutase

Query= SwissProt::O06995
         (226 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS24650 CA265_RS24650
           beta-phosphoglucomutase
          Length = 228

 Score =  172 bits (436), Expect = 5e-48
 Identities = 91/214 (42%), Positives = 129/214 (60%), Gaps = 2/214 (0%)

Query: 1   MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60
           +KA +FDLDGV+ DTA YH+ AWK +A  +   F  + NE+LKG+SR ESL  IL +GG 
Sbjct: 16  IKACLFDLDGVLVDTAVYHYKAWKRLANTMGFDFTEEQNEQLKGVSRVESLNKILAWGGI 75

Query: 61  ETKYTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKIGLASSSRNAP 120
           E   T++EK EL   KN  Y  +I+K+TP ++LPG    L  +     K+ L S+S+N+ 
Sbjct: 76  EK--TDSEKDELAGLKNSWYVDMITKMTPAEVLPGTVDFLTAIHKAGYKLALGSASKNSG 133

Query: 121 KILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAGISAIKS 180
            IL +  +   F  IVD   + K KPDP++FL  A +L  +P +C   EDA AG+ A K 
Sbjct: 134 IILEKTDLAHFFDKIVDGNMVTKSKPDPEVFLKGAELLGFAPDECVVFEDAVAGVEAAKR 193

Query: 181 AGMFAVGVGQGQPMLGADLVVRQTSDLTLELLHE 214
            GM A+G+G+   +  AD+VV     LT++ L E
Sbjct: 194 GGMKAIGIGEKSVLTQADVVVSGLDKLTVKDLEE 227


Lambda     K      H
   0.319    0.136    0.390 

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: 142
Number of extensions: 8
Number of successful extensions: 2
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: 226
Length of database: 228
Length adjustment: 22
Effective length of query: 204
Effective length of database: 206
Effective search space:    42024
Effective search space used:    42024
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 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate CA265_RS24650 CA265_RS24650 (beta-phosphoglucomutase)
to HMM TIGR01990 (pgmB: beta-phosphoglucomutase (EC 5.4.2.6))

# 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/TIGR01990.hmm
# target sequence database:        /tmp/gapView.22230.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01990  [M=187]
Accession:   TIGR01990
Description: bPGM: beta-phosphoglucomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.7e-74  235.3   0.0    3.2e-74  235.0   0.0    1.1  1  lcl|FitnessBrowser__Pedo557:CA265_RS24650  CA265_RS24650 beta-phosphoglucom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS24650  CA265_RS24650 beta-phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.0   0.0   3.2e-74   3.2e-74       1     187 []      16     202 ..      16     202 .. 1.00

  Alignments for each domain:
  == domain 1  score: 235.0 bits;  conditional E-value: 3.2e-74
                                  TIGR01990   1 lkaviFDlDGvitdtaeyhylawkkladelgiefdeelnesLkGvsReesleailkkakkkyseeeke 68 
                                                +ka +FDlDGv++dta yhy+awk+la+ +g  f+ee+ne+LkGvsR esl++il  ++ + +++ek 
  lcl|FitnessBrowser__Pedo557:CA265_RS24650  16 IKACLFDLDGVLVDTAVYHYKAWKRLANTMGFDFTEEQNEQLKGVSRVESLNKILAWGGIEKTDSEKD 83 
                                                799***************************************************************** PP

                                  TIGR01990  69 elaerknekYvellkeltpedvlpgikelleelkkkkikialasasknaklvleklelkdkfdaivda 136
                                                ela  kn+ Yv++++++tp++vlpg +++l+ ++k+++k+al+saskn+ ++lek +l++ fd ivd+
  lcl|FitnessBrowser__Pedo557:CA265_RS24650  84 ELAGLKNSWYVDMITKMTPAEVLPGTVDFLTAIHKAGYKLALGSASKNSGIILEKTDLAHFFDKIVDG 151
                                                ******************************************************************** PP

                                  TIGR01990 137 aevkkgkPdPeiFlaaaeklgvspeecigieDaeaGieaikaagilavgvg 187
                                                + v+k+kPdPe+Fl++ae lg +p+ec+++eDa aG+ea+k++g+ a+g+g
  lcl|FitnessBrowser__Pedo557:CA265_RS24650 152 NMVTKSKPDPEVFLKGAELLGFAPDECVVFEDAVAGVEAAKRGGMKAIGIG 202
                                                *************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (187 nodes)
Target sequences:                          1  (228 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: 8.59
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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