Alignments for a candidate for mmsA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Caulobacter crescentus NA1000

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate CCNA_01360 CCNA_01360 malonate-semialdehyde dehydrogenase IolA

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>FitnessBrowser__Caulo:CCNA_01360
          Length = 500

 Score = 1000 bits (2585), Expect = 0.0
 Identities = 500/500 (100%), Positives = 500/500 (100%)

Query: 1   MMRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAA 60
           MMRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAA
Sbjct: 1   MMRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAA 60

Query: 61  TNPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLL 120
           TNPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLL
Sbjct: 61  TNPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLL 120

Query: 121 KGEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDP 180
           KGEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDP
Sbjct: 121 KGEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDP 180

Query: 181 SVPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGA 240
           SVPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGA
Sbjct: 181 SVPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGA 240

Query: 241 AGKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALR 300
           AGKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALR
Sbjct: 241 AGKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALR 300

Query: 301 EKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGH 360
           EKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGH
Sbjct: 301 EKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGH 360

Query: 361 EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRN 420
           EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRN
Sbjct: 361 EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRN 420

Query: 421 GDAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVT 480
           GDAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVT
Sbjct: 421 GDAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVT 480

Query: 481 QRWPKGGAVLDQSFVIPTMR 500
           QRWPKGGAVLDQSFVIPTMR
Sbjct: 481 QRWPKGGAVLDQSFVIPTMR 500


Lambda     K      H
   0.320    0.137    0.409 

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: 1076
Number of extensions: 31
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: 500
Length of database: 500
Length adjustment: 34
Effective length of query: 466
Effective length of database: 466
Effective search space:   217156
Effective search space used:   217156
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: 52 (24.6 bits)

Align candidate CCNA_01360 CCNA_01360 (malonate-semialdehyde dehydrogenase IolA)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# 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/TIGR01722.hmm
# target sequence database:        /tmp/gapView.18792.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-206  671.5   0.7   3.6e-206  671.3   0.7    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01360  CCNA_01360 malonate-semialdehyde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01360  CCNA_01360 malonate-semialdehyde dehydrogenase IolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.3   0.7  3.6e-206  3.6e-206       2     477 .]       6     483 ..       5     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.3 bits;  conditional E-value: 3.6e-206
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                            h+i+G+ v+g+s+++++v +p t++v a+va asa e+++a+a a+ + aawa t+  +rarv++ ++ ll+
  lcl|FitnessBrowser__Caulo:CCNA_01360   6 PHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRARVMFEFKRLLE 78 
                                           59*********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                            h de+a l+s+e+Gk+++d+kGd+ rGlev+e+ac+v+ ll+Ge ++     +dvys+rqplGvvaGitpfn
  lcl|FitnessBrowser__Caulo:CCNA_01360  79 VHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGEYTQGAGPGIDVYSMRQPLGVVAGITPFN 151
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fpamip+wmf  aia Gn+f+lkpse++ps  v+lael+ eaG+p GvlnvvhGdk+ v+ +l+hpd+kavsf
  lcl|FitnessBrowser__Caulo:CCNA_01360 152 FPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSF 224
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..k 291
                                           vGs+++++ +++++ a gkrvqa++Gaknh++v+pdad+++a+ +++gaa+G+aG+rcma+ ++v vG+    
  lcl|FitnessBrowser__Caulo:CCNA_01360 225 VGSSDIAQSVFQRAGAAGKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKtaT 297
                                           ********************************************************************96447 PP

                             TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364
                                            l e+++ ++  +rvg  +dp a++Gp+++ ++k+r++s+i+ g++eGae+++dGrg+ ++G+eeG fvG+tl
  lcl|FitnessBrowser__Caulo:CCNA_01360 298 ALREKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEGFFVGPTL 370
                                           8889********************************************************************* PP

                             TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437
                                           +++vkp+ + y++eifGpvl +++a++lee+i+l     yGnG aift++G aar+f  ++evG+vG+nvpip
  lcl|FitnessBrowser__Caulo:CCNA_01360 371 FDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDAAREFADQVEVGMVGINVPIP 443
                                           ************************************************************************* PP

                             TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           vp++++sf+Gwk s fGdl+ yG +Gvrfytr+ktvt rw
  lcl|FitnessBrowser__Caulo:CCNA_01360 444 VPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQRW 483
                                           **************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (500 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: 00:00:00.02
# Mc/sec: 8.99
//
[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