Alignments for a candidate for mmsA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Dinoroseobacter shibae DFL-12

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate 3608345 Dshi_1747 methylmalonate-semialdehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__Dino:3608345
          Length = 499

 Score =  652 bits (1683), Expect = 0.0
 Identities = 323/486 (66%), Positives = 381/486 (78%), Gaps = 1/486 (0%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           M ++ HFI G++V G SGRF +V +P TG+VQARV LAS  EL+ A+A A  AQ AWAAT
Sbjct: 1   MEELSHFINGKRVAGTSGRFADVMNPATGEVQARVPLASPEELDAAVAAAAAAQPAWAAT 60

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARV+ EF RLL   MD+LA  LS EHGK + D+KGD+ RGLEV+EF  G PHLLK
Sbjct: 61  NPQRRARVLMEFVRLLNRDMDKLAEALSREHGKTLPDAKGDVVRGLEVVEFCIGAPHLLK 120

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GE+T  AGPGID+YSMRQ LGVVAGITPFNFPAMIPMW   PA+A GNAFILKPSERDPS
Sbjct: 121 GEFTDSAGPGIDMYSMRQALGVVAGITPFNFPAMIPMWKMAPALACGNAFILKPSERDPS 180

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VP+ LAELM EAGLP G+L V++GDK  V+AILD+  I+A+ FVGS+ IA+ ++ R  A 
Sbjct: 181 VPLMLAELMTEAGLPDGLLQVINGDKGAVDAILDNDTIQAIGFVGSTPIAEYIYSRGCAN 240

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKRVQ  GGAKNH ++MPDADLDQA   ++GA YG+AGERCMA+ V VPVGE+TA  L E
Sbjct: 241 GKRVQCFGGAKNHMIIMPDADLDQAADALVGAGYGAAGERCMAISVAVPVGEETADRLIE 300

Query: 302 KLVAAIGGLRVGVSTD-PDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGH 360
           KLV  +  L+VG  T   D  YGPVV+AA KA IE  +Q GVD+GA+LVVDGR FSLQG+
Sbjct: 301 KLVPRVEALKVGPYTSGTDVDYGPVVTAAAKANIERLVQSGVDQGAKLVVDGRDFSLQGY 360

Query: 361 EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRN 420
           E GFFVGP LFD+V      Y  EIFGPVL  VRA+S EE + LA  H+YGNG AIFTR+
Sbjct: 361 ENGFFVGPHLFDNVSKEMDIYRTEIFGPVLCTVRAKSYEEALGLAMDHEYGNGTAIFTRD 420

Query: 421 GDAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVT 480
           GDAAR+FA+++ +GMVGINVPIPVP+AYH+FGGWK+SGFGDLNQ+G D  RFYTRTKTVT
Sbjct: 421 GDAARDFANRINIGMVGINVPIPVPLAYHTFGGWKKSGFGDLNQHGPDAFRFYTRTKTVT 480

Query: 481 QRWPKG 486
            RWP G
Sbjct: 481 ARWPSG 486


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: 853
Number of extensions: 24
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: 500
Length of database: 499
Length adjustment: 34
Effective length of query: 466
Effective length of database: 465
Effective search space:   216690
Effective search space used:   216690
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 3608345 Dshi_1747 (methylmalonate-semialdehyde dehydrogenase (RefSeq))
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.2701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.5e-198  644.4   0.0   6.2e-198  644.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608345  Dshi_1747 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608345  Dshi_1747 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.2   0.0  6.2e-198  6.2e-198       2     477 .]       5     483 ..       4     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 644.2 bits;  conditional E-value: 6.2e-198
                         TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                        h+i+Gk v g+s+++ +v npat+ev a+v+ as ee+daava+a  + +awa t+  +rarvl+ +  ll+ + d
  lcl|FitnessBrowser__Dino:3608345   5 SHFINGKRVAGTSGRFADVMNPATGEVQARVPLASPEELDAAVAAAAAAQPAWAATNPQRRARVLMEFVRLLNRDMD 81 
                                       69*************************************************************************** PP

                         TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplw 155
                                       ++a+ +s e+Gktl dakGdv+rGlevve+  + + ll+Ge ++s    +d+ys+rq lGvvaGitpfnfpamip+w
  lcl|FitnessBrowser__Dino:3608345  82 KLAEALSREHGKTLPDAKGDVVRGLEVVEFCIGAPHLLKGEFTDSAGPGIDMYSMRQALGVVAGITPFNFPAMIPMW 158
                                       ***************************************************************************** PP

                         TIGR01722 156 mfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiye 232
                                        +  a+acGn+f+lkpse++ps  + lael++eaG+pdG l+v+ Gdk avd +l+   ++a+ fvGs++++eyiy+
  lcl|FitnessBrowser__Dino:3608345 159 KMAPALACGNAFILKPSERDPSVPLMLAELMTEAGLPDGLLQVINGDKGAVDAILDNDTIQAIGFVGSTPIAEYIYS 235
                                       ***************************************************************************** PP

                         TIGR01722 233 tgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvg 307
                                       +g+a+gkrvq+++Gaknhm+++pdad+++a+dalvga +GaaG+rcmais+av vG+   ++l+e+++ r+e ++vg
  lcl|FitnessBrowser__Dino:3608345 236 RGCANGKRVQCFGGAKNHMIIMPDADLDQAADALVGAGYGAAGERCMAISVAVPVGEEtaDRLIEKLVPRVEALKVG 312
                                       ********************************************************85459**************** PP

                         TIGR01722 308 agdd.pgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpv 383
                                       +++  +  ++Gp++t +ak+++++l++sg+++Ga++++dGr + ++Gye+G fvG+ l+++v  +m iy+ eifGpv
  lcl|FitnessBrowser__Dino:3608345 313 PYTSgTDVDYGPVVTAAAKANIERLVQSGVDQGAKLVVDGRDFSLQGYENGFFVGPHLFDNVSKEMDIYRTEIFGPV 389
                                       *99724689******************************************************************** PP

                         TIGR01722 384 lvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyG 460
                                       l+ ++a ++eea+ l  +  yGnGtaift+dG aar f  +i++G+vG+nvpipvpl++++f+Gwk+s fGdl+ +G
  lcl|FitnessBrowser__Dino:3608345 390 LCTVRAKSYEEALGLAMDHEYGNGTAIFTRDGDAARDFANRINIGMVGINVPIPVPLAYHTFGGWKKSGFGDLNQHG 466
                                       ***************************************************************************** PP

                         TIGR01722 461 kqGvrfytrlktvtarw 477
                                        +  rfytr+ktvtarw
  lcl|FitnessBrowser__Dino:3608345 467 PDAFRFYTRTKTVTARW 483
                                       ***************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (499 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.61
//
[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