GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Rhodococcus qingshengii djl-6-2

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_050654861.1 C1M55_RS10170 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_002893965.1:WP_050654861.1
          Length = 501

 Score =  556 bits (1433), Expect = e-163
 Identities = 280/497 (56%), Positives = 359/497 (72%), Gaps = 4/497 (0%)

Query: 3   LIKHLIGGELIADTGR-TADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPP 61
           +I H + G+  A T   TA V NP+TG+   ++ LA+ E  +  IDAA AAFPAWR+T  
Sbjct: 8   VIAHWLDGKPFAGTSEDTAPVTNPATGQITGRLALANLEDARAVIDAAAAAFPAWRDTSL 67

Query: 62  AKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE 121
           A+R QVLF F++LL A +  + ++I+ EHGK + DA GE+ RG E VE+A   P +LKG 
Sbjct: 68  ARRTQVLFSFRELLNARKGELAEIITAEHGKVLSDALGEISRGQEVVEFACGIPHLLKGG 127

Query: 122 YSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSST 181
           Y+ N    +D +S  QP+G V  I+PFNFPAMVP+W +P+AIA GNT ILKPSE+DP++ 
Sbjct: 128 YTENASTKVDVYSIRQPLGPVGIISPFNFPAMVPMWFFPVAIAAGNTVILKPSEKDPTAA 187

Query: 182 LLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGK 241
           + +AEL+ EAGLP GV NV+ GDK AVD L+E   VKA+SFVGSTPIA+Y+Y+ GT  GK
Sbjct: 188 IWLAELWAEAGLPPGVFNVLQGDKLAVDELLENKAVKAISFVGSTPIAQYVYATGTANGK 247

Query: 242 RVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL 301
           RVQALGGAKNHA+++PDADLD A  A++ A +GS GERCMAIS  V VGD IAD LV K+
Sbjct: 248 RVQALGGAKNHAIVLPDADLDLAADAMVNAGFGSAGERCMAISALVAVGD-IADELVAKI 306

Query: 302 VPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENG 361
           V +   L  G GT    DMGPLVT A RDKV  Y+D G   GA +VVDGR  +  G  +G
Sbjct: 307 VERTTPLVTGDGTK-NSDMGPLVTKAHRDKVASYVDAGEKDGATIVVDGRTVQADGGPDG 365

Query: 362 FFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEA 421
           F+LG TL D VT +M+IY +EIFGPVL +VRV++ ++A++LIN++ YGNGT IFT DG A
Sbjct: 366 FWLGPTLIDHVTTDMSIYTDEIFGPVLSVVRVDTYDQALELINNNPYGNGTAIFTNDGGA 425

Query: 422 ARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481
           AR F +E+EVGM+G+NVP+PVP+AY+SFGGWK SLFGD HA+G +GV F+T+ KA+T RW
Sbjct: 426 ARRFQNEVEVGMIGINVPIPVPMAYYSFGGWKNSLFGDTHAHGTEGVHFFTRGKAVTSRW 485

Query: 482 PQRKSHEAAQFAFPSNS 498
               SH      FP NS
Sbjct: 486 LD-PSHGGINLGFPENS 501


Lambda     K      H
   0.319    0.137    0.411 

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: 732
Number of extensions: 28
Number of successful extensions: 3
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: 498
Length of database: 501
Length adjustment: 34
Effective length of query: 464
Effective length of database: 467
Effective search space:   216688
Effective search space used:   216688
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_050654861.1 C1M55_RS10170 (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.1201628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-210  686.4   0.4   1.2e-210  686.2   0.4    1.0  1  NCBI__GCF_002893965.1:WP_050654861.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050654861.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.2   0.4  1.2e-210  1.2e-210       2     477 .]      10     485 ..       9     485 .. 0.99

  Alignments for each domain:
  == domain 1  score: 686.2 bits;  conditional E-value: 1.2e-210
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                            h++dGk   g+s+   pv+npat+++++++a a  e+  a + +a  +f+aw++ts+a+r++vl+ +++ll+
  NCBI__GCF_002893965.1:WP_050654861.1  10 AHWLDGKPFAGTSEDTAPVTNPATGQITGRLALANLEDARAVIDAAAAAFPAWRDTSLARRTQVLFSFRELLN 82 
                                           79*********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                           +++ e+a++i+ae+Gk+l+da G++ rG evve+ac+++ ll+G  +e+ +++vdvysirqplG v  i+pfn
  NCBI__GCF_002893965.1:WP_050654861.1  83 ARKGELAEIITAEHGKVLSDALGEISRGQEVVEFACGIPHLLKGGYTENASTKVDVYSIRQPLGPVGIISPFN 155
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fpam+p+w fp+aia Gnt +lkpsek+p+aa+ lael+ eaG+p Gv+nv+ Gdk avd+lle   vka+sf
  NCBI__GCF_002893965.1:WP_050654861.1 156 FPAMVPMWFFPVAIAAGNTVILKPSEKDPTAAIWLAELWAEAGLPPGVFNVLQGDKLAVDELLENKAVKAISF 228
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.ke 292
                                           vGs+++++y+y tg+a+gkrvqal+Gaknh++vlpdad++ a+da+v+a +G+aG+rcmaisa v+vG++ +e
  NCBI__GCF_002893965.1:WP_050654861.1 229 VGSTPIAQYVYATGTANGKRVQALGGAKNHAIVLPDADLDLAADAMVNAGFGSAGERCMAISALVAVGDIaDE 301
                                           ********************************************************************988** PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           lv +i+er   +  g g++ ++++Gpl+tk+++++vas++++g k+Ga +++dGr+++ +G ++G ++G+tl+
  NCBI__GCF_002893965.1:WP_050654861.1 302 LVAKIVERTTPLVTGDGTK-NSDMGPLVTKAHRDKVASYVDAGEKDGATIVVDGRTVQADGGPDGFWLGPTLI 373
                                           ***************9997.579************************************************** PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++v +dm+iy +eifGpvl v+++dt+++a++lin++pyGnGtaift+dG+aar+fq e+evG++G+nvpipv
  NCBI__GCF_002893965.1:WP_050654861.1 374 DHVTTDMSIYTDEIFGPVLSVVRVDTYDQALELINNNPYGNGTAIFTNDGGAARRFQNEVEVGMIGINVPIPV 446
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           p++++sf+Gwk+slfGd+h++G +Gv+f+tr+k+vt+rw
  NCBI__GCF_002893965.1:WP_050654861.1 447 PMAYYSFGGWKNSLFGDTHAHGTEGVHFFTRGKAVTSRW 485
                                           *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 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: 00:00:00.21
# Mc/sec: 1.09
//
[ok]

This GapMind analysis is from Sep 24 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