Alignments for a candidate for rhaD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaD in Escherichia coli BW25113

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate 17942 b3902 rhamnulose-1-phosphate aldolase (NCBI)

Query= BRENDA::P32169
         (274 letters)



>FitnessBrowser__Keio:17942
          Length = 274

 Score =  565 bits (1455), Expect = e-166
 Identities = 274/274 (100%), Positives = 274/274 (100%)

Query: 1   MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQ 60
           MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQ
Sbjct: 1   MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQ 60

Query: 61  PMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPA 120
           PMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPA
Sbjct: 61  PMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPA 120

Query: 121 HFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGV 180
           HFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGV
Sbjct: 121 HFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGV 180

Query: 181 GILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVK 240
           GILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVK
Sbjct: 181 GILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVK 240

Query: 241 VYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
           VYSMGGMKQTISREELIALGKRFGVTPLASALAL
Sbjct: 241 VYSMGGMKQTISREELIALGKRFGVTPLASALAL 274


Lambda     K      H
   0.320    0.136    0.425 

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: 404
Number of extensions: 3
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: 274
Length of database: 274
Length adjustment: 25
Effective length of query: 249
Effective length of database: 249
Effective search space:    62001
Effective search space used:    62001
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: 47 (22.7 bits)

Align candidate 17942 b3902 (rhamnulose-1-phosphate aldolase (NCBI))
to HMM TIGR02624 (rhaD: rhamnulose-1-phosphate aldolase (EC 4.1.2.19))

# 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/TIGR02624.hmm
# target sequence database:        /tmp/gapView.27104.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02624  [M=270]
Accession:   TIGR02624
Description: rhamnu_1P_ald: rhamnulose-1-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.9e-145  469.1   0.0   2.2e-145  469.0   0.0    1.0  1  lcl|FitnessBrowser__Keio:17942  b3902 rhamnulose-1-phosphate ald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17942  b3902 rhamnulose-1-phosphate aldolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.0   0.0  2.2e-145  2.2e-145       1     270 []       1     272 [.       1     272 [. 0.99

  Alignments for each domain:
  == domain 1  score: 469.0 bits;  conditional E-value: 2.2e-145
                       TIGR02624   1 mqdildavfvkemikttedlyrkGwdernGGnislrlkeeeveayld.lkqvlrkiplkfdakelankyflvtGsGkyf 78 
                                     mq+i++++fv++mik+t+d++ kGwdernGGn++lrl+++++++y+d ++q++r+ipl+++++ lan+ f+vtGsGk+f
  lcl|FitnessBrowser__Keio:17942   1 MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDnFHQQPRYIPLSQPMPLLANTPFIVTGSGKFF 79 
                                     79********************************************99******************************* PP

                       TIGR02624  79 knveeapaenlgllrvsedGksvellwGltdgglptselpahflshiarlkvdp.enrvimhchatnlialtftlelde 156
                                     +nv+ +pa+nlg+++v++dG+ +++lwGlt++++ptselpahflsh++r+k+++ ++rvimhchatnlialt++le+d+
  lcl|FitnessBrowser__Keio:17942  80 RNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNgKDRVIMHCHATNLIALTYVLENDT 158
                                     ****************************************************998************************ PP

                       TIGR02624 157 kaftrtlwemsteclvvfpeGvGiipwlvpGtdeiGeataekmkesrlvlwphhGifgaGesldevfGlietaekaaev 235
                                     ++ftr+lwe+steclvvfp+GvGi+pw+vpGtdeiG+ata++m++++lvlwp+hG+fg+G++lde+fGli+taek+a+v
  lcl|FitnessBrowser__Keio:17942 159 AVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQV 237
                                     ******************************************************************************* PP

                       TIGR02624 236 ytkvlsqggvkqtisdedlialaerfdvkpkakyl 270
                                     ++kv+s+gg+kqtis+e+lial++rf+v+p a++l
  lcl|FitnessBrowser__Keio:17942 238 LVKVYSMGGMKQTISREELIALGKRFGVTPLASAL 272
                                     ******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (274 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: 10.40
//
[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