Alignments for a candidate for mmsA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Sphingomonas koreensis DSMZ 15582

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate Ga0059261_3677 Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase

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



>FitnessBrowser__Korea:Ga0059261_3677
          Length = 503

 Score =  775 bits (2002), Expect = 0.0
 Identities = 384/498 (77%), Positives = 427/498 (85%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           +R+I HFIG     G   R  +VFDPNTG VQA+V L +  +L+ A+ANA  AQ +WAAT
Sbjct: 5   VREISHFIGNAATAGTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAAT 64

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARVMF FK L+E +M+ELA LLSSEHGKVIAD+KGDIQRGLEVIEF CG+PH+LK
Sbjct: 65  NPQRRARVMFNFKALIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLK 124

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFG AIA GNAFILKPSERDPS
Sbjct: 125 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPS 184

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VPVRLAELM+EAGLP GVL VV GDK+ V+AILDHP+IKAVSFVGSSDIA  V++R  AA
Sbjct: 185 VPVRLAELMLEAGLPEGVLQVVQGDKEMVDAILDHPEIKAVSFVGSSDIAHYVYRRGVAA 244

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKRVQAMGGAKNHG+VMPDADLDQ V D+ GAA+GSAGERCMALPVVVPVG+KTA ALR 
Sbjct: 245 GKRVQAMGGAKNHGIVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGDKTADALRA 304

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           KL+ AI  LRVGVSTD  AHYGPVV+AAHKA+IESYIQMGVDEGAELVVDGRGF+LQGHE
Sbjct: 305 KLLPAIEALRVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVVDGRGFTLQGHE 364

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
           +GFFVGPTLFD V P  +SY +EIFGPVLQ+VRA   E  + L S HQYGNGVAIFTRNG
Sbjct: 365 QGFFVGPTLFDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTRNG 424

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
            AAREFA +V VGMVGINVPIPVPVAYH+FGGWKRS FGD NQ+GM+G++F+T+ KTVTQ
Sbjct: 425 HAAREFAARVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTVTQ 484

Query: 482 RWPKGGAVLDQSFVIPTM 499
           RWP G      +FVIPTM
Sbjct: 485 RWPDGSPDGGNAFVIPTM 502


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: 908
Number of extensions: 30
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: 503
Length adjustment: 34
Effective length of query: 466
Effective length of database: 469
Effective search space:   218554
Effective search space used:   218554
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 Ga0059261_3677 Ga0059261_3677 (methylmalonic acid semialdehyde dehydrogenase)
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.1873810.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-202  657.9   2.6     5e-202  657.7   2.6    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3677  Ga0059261_3677 methylmalonic aci


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3677  Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.7   2.6    5e-202    5e-202       2     477 .]       9     486 ..       8     486 .. 0.99

  Alignments for each domain:
  == domain 1  score: 657.7 bits;  conditional E-value: 5e-202
                                 TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                                h+i+ +   g+++++ +v +p t+ v a+v+  +++++daa+a a ++  +wa t+  +rarv++ ++
  lcl|FitnessBrowser__Korea:Ga0059261_3677   9 SHFIGNAATAGTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAATNPQRRARVMFNFK 77 
                                               79******************************************************************* PP

                                 TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGv 139
                                               al++++ +e+a+l+s+e+Gk+++dakGd+ rGlev+e+ c+++  l+Ge ++     +dvys+rqplGv
  lcl|FitnessBrowser__Korea:Ga0059261_3677  78 ALIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLKGEYTQGAGPGIDVYSMRQPLGV 146
                                               ********************************************************************* PP

                                 TIGR01722 140 vaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdr 208
                                               vaGitpfnfpamip+wmf +aiacGn+f+lkpse++ps  v+lael++eaG+p+Gvl+vv Gdke vd 
  lcl|FitnessBrowser__Korea:Ga0059261_3677 147 VAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPSVPVRLAELMLEAGLPEGVLQVVQGDKEMVDA 215
                                               ********************************************************************* PP

                                 TIGR01722 209 llehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqr 277
                                               +l+hp++kavsfvGs+++++y+y++g a gkrvqa++Gaknh++v+pdad+++++++l gaa+G+aG+r
  lcl|FitnessBrowser__Korea:Ga0059261_3677 216 ILDHPEIKAVSFVGSSDIAHYVYRRGVAAGKRVQAMGGAKNHGIVMPDADLDQVVNDLAGAAFGSAGER 284
                                               ********************************************************************* PP

                                 TIGR01722 278 cmaisaavlvGaa..kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevll 344
                                               cma+ ++v vG+   + l  ++  ++e +rvg  +d+ga++Gp++t ++k++++s+i+ g++eGae+++
  lcl|FitnessBrowser__Korea:Ga0059261_3677 285 CMALPVVVPVGDKtaDALRAKLLPAIEALRVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVV 353
                                               ***********854488999************************************************* PP

                                 TIGR01722 345 dGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaifts 413
                                               dGrg++++G+e+G fvG+tl++rv p+m+ y+eeifGpvl +++a  +e a++l  e  yGnG aift+
  lcl|FitnessBrowser__Korea:Ga0059261_3677 354 DGRGFTLQGHEQGFFVGPTLFDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTR 422
                                               ********************************************************************* PP

                                 TIGR01722 414 dGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               +G aar+f  +++vG+vG+nvpipvp+++++f+Gwk s fGd++ +G +G++f+t++ktvt rw
  lcl|FitnessBrowser__Korea:Ga0059261_3677 423 NGHAAREFAARVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTVTQRW 486
                                               **************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (503 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: 00:00:00.01
# Mc/sec: 22.11
//
[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