Alignments for a candidate for mmsA in Phaeobacter inhibens BS107

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.3704.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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.07
//
[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