GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Rhizobium freirei PRF 81

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_004109547.1 RHSP_RS04195 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_000359745.1:WP_004109547.1
          Length = 498

 Score =  673 bits (1737), Expect = 0.0
 Identities = 332/500 (66%), Positives = 392/500 (78%), Gaps = 3/500 (0%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           MR+I HFIGG++V G SGR   V++P TG+VQA VALAS  EL  A+ANAK AQ  W AT
Sbjct: 1   MREIGHFIGGKRVAGTSGRTSNVYNPATGEVQATVALASVDELRAAVANAKAAQPKWGAT 60

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARV F F  LL  +MDELA LLSSEHGK + DSKGDI RGLEV EF CG+PHL K
Sbjct: 61  NPQRRARVFFRFVELLNQNMDELATLLSSEHGKTVEDSKGDIIRGLEVCEFVCGIPHLQK 120

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GE+T+GAGP ID+YS+RQP+GV AGITPFNFP MIPMWMF PAIA GNAFILKPSERDPS
Sbjct: 121 GEFTEGAGPAIDMYSIRQPVGVGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           +P+RLAELMIEAGLP G+LNVV+GDK  V+AIL  PDI AVSFVGS+ IA+ V+  A   
Sbjct: 181 LPIRLAELMIEAGLPAGILNVVNGDKTAVDAILTDPDIAAVSFVGSTPIARYVYGTAAMN 240

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKR Q  GGAKNH ++MPDAD+DQAV  ++GA YGSAGERCMA+ V VPVGE TA  L E
Sbjct: 241 GKRAQCFGGAKNHMIIMPDADMDQAVNALMGAGYGSAGERCMAVSVAVPVGEDTANRLVE 300

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           KLV  I  LR+G  TD  A  GP+V+     R+   I  GV+EGA+LVVDGRGF LQG+E
Sbjct: 301 KLVPKIESLRIGPYTDDKADMGPLVTKEAYNRVNGLIDRGVEEGAKLVVDGRGFKLQGYE 360

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
           EG+FVG TLFDHVKP    Y  EIFGPVL +VRA++ EE + L  +H+YGNGVAI+TR+G
Sbjct: 361 EGYFVGGTLFDHVKPDMDIYKTEIFGPVLSVVRAKNYEEALELPMKHEYGNGVAIYTRDG 420

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
           DAAR+FA ++ +GM+G+NVPIPVP+AYHSFGGWK S FGDLNQ+G D ++F+TRTKT+T 
Sbjct: 421 DAARDFASRINIGMIGVNVPIPVPLAYHSFGGWKASSFGDLNQHGTDSIKFWTRTKTITA 480

Query: 482 RWPKGGAVLD-QSFVIPTMR 500
           RWP G  + D   FV+PTM+
Sbjct: 481 RWPSG--IKDGAEFVMPTMK 498


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: 844
Number of extensions: 27
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: 498
Length adjustment: 34
Effective length of query: 466
Effective length of database: 464
Effective search space:   216224
Effective search space used:   216224
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 WP_004109547.1 RHSP_RS04195 (CoA-acylating 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.1929838.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-203  662.5   0.2   1.9e-203  662.4   0.2    1.0  1  NCBI__GCF_000359745.1:WP_004109547.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359745.1:WP_004109547.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  662.4   0.2  1.9e-203  1.9e-203       2     477 .]       5     482 ..       4     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 662.4 bits;  conditional E-value: 1.9e-203
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                            h+i+Gk v g+s++  +v npat+ev a va as++e+ aava a+ + + w+ t+  +rarv++r+ +ll+
  NCBI__GCF_000359745.1:WP_004109547.1   5 GHFIGGKRVAGTSGRTSNVYNPATGEVQATVALASVDELRAAVANAKAAQPKWGATNPQRRARVFFRFVELLN 77 
                                           59*********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                           ++ de+a l+s+e+Gkt+ed+kGd++rGlev e+ c+++ l +Ge +e     +d+ysirqp+Gv aGitpfn
  NCBI__GCF_000359745.1:WP_004109547.1  78 QNMDELATLLSSEHGKTVEDSKGDIIRGLEVCEFVCGIPHLQKGEFTEGAGPAIDMYSIRQPVGVGAGITPFN 150
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fp mip+wmf  aiacGn+f+lkpse++ps  ++lael+ eaG+p G+lnvv Gdk avd +l  pd+ avsf
  NCBI__GCF_000359745.1:WP_004109547.1 151 FPGMIPMWMFAPAIACGNAFILKPSERDPSLPIRLAELMIEAGLPAGILNVVNGDKTAVDAILTDPDIAAVSF 223
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..k 291
                                           vGs+++++y+y t++ +gkr q+++Gaknhm+++pdad ++a++al+ga +G+aG+rcma+s+av vG+   +
  NCBI__GCF_000359745.1:WP_004109547.1 224 VGSTPIARYVYGTAAMNGKRAQCFGGAKNHMIIMPDADMDQAVNALMGAGYGSAGERCMAVSVAVPVGEDtaN 296
                                           ********************************************************************85449 PP

                             TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364
                                           +lve+++ ++e +r+g+++d  a++Gpl+tk+a +rv+ li+ g++eGa++++dGrg+k++GyeeG fvG tl
  NCBI__GCF_000359745.1:WP_004109547.1 297 RLVEKLVPKIESLRIGPYTDDKADMGPLVTKEAYNRVNGLIDRGVEEGAKLVVDGRGFKLQGYEEGYFVGGTL 369
                                           9************************************************************************ PP

                             TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437
                                           +++vkpdm iyk eifGpvl v++a  +eea++l  +  yGnG ai+t+dG aar f  +i++G++Gvnvpip
  NCBI__GCF_000359745.1:WP_004109547.1 370 FDHVKPDMDIYKTEIFGPVLSVVRAKNYEEALELPMKHEYGNGVAIYTRDGDAARDFASRINIGMIGVNVPIP 442
                                           ************************************************************************* PP

                             TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           vpl+++sf+Gwk+s fGdl+ +G + ++f+tr+kt+tarw
  NCBI__GCF_000359745.1:WP_004109547.1 443 VPLAYHSFGGWKASSFGDLNQHGTDSIKFWTRTKTITARW 482
                                           **************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (498 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: 13.44
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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