GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Phaeobacter inhibens BS107

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate GFF1706 PGA1_c17300 methylmalonate-semialdehyde dehydrogenase

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



>FitnessBrowser__Phaeo:GFF1706
          Length = 499

 Score =  609 bits (1571), Expect = e-179
 Identities = 304/486 (62%), Positives = 361/486 (74%), Gaps = 1/486 (0%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           M+++ HFI G+ V G SGRF +VF+P TG VQ +  +ASA E    I  A  AQ AW AT
Sbjct: 1   MKELGHFINGKLVSGTSGRFDDVFNPATGDVQYQCPMASAAETTDIIEKAAAAQPAWGAT 60

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQ+RARVM +   L+   MD+LA  LS EHGK I D+KGD+QRGLEVIE+  G P +LK
Sbjct: 61  NPQKRARVMMKMVALMNRDMDKLAEALSREHGKTIPDAKGDLQRGLEVIEYCVGAPQMLK 120

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GE+T  AGPGID+YSMRQPLGVV  I PFNFPAM+P+W  GPA+A GNA +LKPSERDPS
Sbjct: 121 GEFTDSAGPGIDMYSMRQPLGVVGSIMPFNFPAMMPLWHVGPALACGNAVVLKPSERDPS 180

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VP+ LAEL +EAGLP GV  VV+GDK+ V+ ILD   I+ VSFVGS+ IAQ ++ RA A 
Sbjct: 181 VPLMLAELFVEAGLPEGVFQVVNGDKEAVDTILDSEIIQGVSFVGSTPIAQYIYSRATAN 240

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKR Q  GGAKNH +VMPDADLD A   ++GA +G+AGERCMA+ V VPVGE+TA  L E
Sbjct: 241 GKRAQCFGGAKNHMIVMPDADLDLAADALVGAGFGAAGERCMAISVAVPVGEETADKLIE 300

Query: 302 KLVAAIGGLRVGVST-DPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGH 360
           KL+  I  L+VG  T   D   GPVV+AA K RI   IQ GVD+GA+LVVD R F LQG+
Sbjct: 301 KLIPRIEKLKVGPYTAGDDVDLGPVVTAASKERILGLIQSGVDQGAKLVVDNRDFKLQGY 360

Query: 361 EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRN 420
           E+GFFVG  LFDHV P    Y  EIFGPVL  VRA S E+ + LA  H+YGNG AIFTR+
Sbjct: 361 EDGFFVGAHLFDHVTPDMDIYKQEIFGPVLSTVRANSYEDALKLAMDHEYGNGTAIFTRD 420

Query: 421 GDAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVT 480
           GD AR+FA +V +GMVGINVPIPVP+AYH+FGGWK+S FGDLNQ+G D  +FYTRTKTVT
Sbjct: 421 GDTARDFASRVNIGMVGINVPIPVPLAYHTFGGWKKSMFGDLNQHGPDSFKFYTRTKTVT 480

Query: 481 QRWPKG 486
            RWP G
Sbjct: 481 SRWPSG 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: 804
Number of extensions: 27
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 GFF1706 PGA1_c17300 (methylmalonate-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.3037716.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.9e-188  611.3   0.1   6.7e-188  611.1   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1706  PGA1_c17300 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1706  PGA1_c17300 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.1   0.1  6.7e-188  6.7e-188       3     477 .]       6     483 ..       4     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 611.1 bits;  conditional E-value: 6.7e-188
                          TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                        h+i+Gk+v g+s+++ +v npat++v  + ++asa+e    +  a  + +aw+ t+  +rarv+++  al++ + d
  lcl|FitnessBrowser__Phaeo:GFF1706   6 HFINGKLVSGTSGRFDDVFNPATGDVQYQCPMASAAETTDIIEKAAAAQPAWGATNPQKRARVMMKMVALMNRDMD 81 
                                        9*************************************************************************** PP

                          TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamipl 154
                                        ++a+ +s e+Gkt+ dakGd+ rGlev+e+  + + +l+Ge ++s    +d+ys+rqplGvv  i pfnfpam+pl
  lcl|FitnessBrowser__Phaeo:GFF1706  82 KLAEALSREHGKTIPDAKGDLQRGLEVIEYCVGAPQMLKGEFTDSAGPGIDMYSMRQPLGVVGSIMPFNFPAMMPL 157
                                        **************************************************************************** PP

                          TIGR01722 155 wmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyi 230
                                        w    a+acGn+ vlkpse++ps  + lael+ eaG+p+Gv++vv Gdkeavd++l+   ++ vsfvGs+++++yi
  lcl|FitnessBrowser__Phaeo:GFF1706 158 WHVGPALACGNAVVLKPSERDPSVPLMLAELFVEAGLPEGVFQVVNGDKEAVDTILDSEIIQGVSFVGSTPIAQYI 233
                                        **************************************************************************** PP

                          TIGR01722 231 yetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekv 304
                                        y++++a+gkr q+++Gaknhm+v+pdad++ a+dalvga +GaaG+rcmais+av vG+   ++l+e++  r+ek+
  lcl|FitnessBrowser__Phaeo:GFF1706 234 YSRATANGKRAQCFGGAKNHMIVMPDADLDLAADALVGAGFGAAGERCMAISVAVPVGEEtaDKLIEKLIPRIEKL 309
                                        **********************************************************85459************* PP

                          TIGR01722 305 rvgagddp.gaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeei 379
                                        +vg+++     +lGp++t ++ker+  li+sg+++Ga++++d r +k++Gye+G fvG  l+++v pdm iyk+ei
  lcl|FitnessBrowser__Phaeo:GFF1706 310 KVGPYTAGdDVDLGPVVTAASKERILGLIQSGVDQGAKLVVDNRDFKLQGYEDGFFVGAHLFDHVTPDMDIYKQEI 385
                                        ****9875268***************************************************************** PP

                          TIGR01722 380 fGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455
                                        fGpvl  ++a+++e+a+kl  +  yGnGtaift+dG +ar f  ++++G+vG+nvpipvpl++++f+Gwk+s+fGd
  lcl|FitnessBrowser__Phaeo:GFF1706 386 FGPVLSTVRANSYEDALKLAMDHEYGNGTAIFTRDGDTARDFASRVNIGMVGINVPIPVPLAYHTFGGWKKSMFGD 461
                                        **************************************************************************** PP

                          TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477
                                        l+ +G +  +fytr+ktvt+rw
  lcl|FitnessBrowser__Phaeo:GFF1706 462 LNQHGPDSFKFYTRTKTVTSRW 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.02
//
[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:

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