Alignments for a candidate for mmsA in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Methylobacterium nodulans ORS 2060

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_015929170.1 MNOD_RS12075 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>NCBI__GCF_000022085.1:WP_015929170.1
          Length = 499

 Score =  630 bits (1625), Expect = 0.0
 Identities = 305/496 (61%), Positives = 381/496 (76%), Gaps = 2/496 (0%)

Query: 4   IGHLINGQ-LVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPL 62
           I H I G+ L   + RS  VFNPATGE    + LA    V+ A++AA  AFP W  TPPL
Sbjct: 5   IDHFIGGRRLAGRSGRSAPVFNPATGEQTGAVALADGSEVDAAVTAAAAAFPAWARTPPL 64

Query: 63  KRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEH 122
           +RAR++ +F +++E   D +  +I  EHGK+  DA GE+QRG+E +E+A GAP+LLKGE 
Sbjct: 65  RRARILNKFLQIIEDRIDSLAAVITAEHGKVLSDAKGEIQRGMEVIEFAVGAPQLLKGEV 124

Query: 123 SRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTL 182
           + NVG  +DS +  QP+GVVAGITPFNFPVMVP+WMFP+A+ CGNCFVLKPSERDPS++L
Sbjct: 125 TENVGTRVDSHALRQPLGVVAGITPFNFPVMVPMWMFPVALACGNCFVLKPSERDPSASL 184

Query: 183 YIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKR 242
            +A+ L+EAGLPDGV NVV+GDKEAVDALLH  +V  VSFVGSTPIA YIY TA+ANGKR
Sbjct: 185 LLAEWLKEAGLPDGVFNVVHGDKEAVDALLHHPKVAGVSFVGSTPIARYIYATATANGKR 244

Query: 243 CQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMT 302
            QALGGAKNH I+MPDADMD AV+ L+GAA+GS+GERCMA+SVAV VG+   + LV ++ 
Sbjct: 245 AQALGGAKNHMIIMPDADMDQAVDALMGAAYGSAGERCMAVSVAVPVGEKTANTLVERLI 304

Query: 303 QAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENGF 362
             ++ LKVGP TD  ++ GP++TRQH +KV GYI     +GA ++VDGR  K+  +E GF
Sbjct: 305 PKVRALKVGPGTDRDSEMGPLVTRQHLDKVRGYIAQGVSEGAKLLVDGRDLKLQGYETGF 364

Query: 363 FVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEAA 422
           F+GGTL DHVTPEMT Y+EEIFGPVL V R      A  LI+ HE+GNGT IFTRDG+AA
Sbjct: 365 FIGGTLFDHVTPEMTIYKEEIFGPVLAVTRAPDYATAARLINEHEFGNGTAIFTRDGDAA 424

Query: 423 RYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRWP 482
           R F+  IQVGMVGIN+P+PVP+A+HSFGGWK SLFGD H +GP+ VRFYT+ K +T RWP
Sbjct: 425 REFAHEIQVGMVGINVPIPVPMAFHSFGGWKASLFGDHHMHGPEGVRFYTRLKAITTRWP 484

Query: 483 SAGVREGAEFSMPTMK 498
           + G+R GA+F MPTM+
Sbjct: 485 T-GIRAGADFVMPTME 499


Lambda     K      H
   0.319    0.135    0.405 

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: 741
Number of extensions: 25
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: 498
Length of database: 499
Length adjustment: 34
Effective length of query: 464
Effective length of database: 465
Effective search space:   215760
Effective search space used:   215760
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_015929170.1 MNOD_RS12075 (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.968918.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-214  698.9   0.1   1.8e-214  698.7   0.1    1.0  1  NCBI__GCF_000022085.1:WP_015929170.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015929170.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  698.7   0.1  1.8e-214  1.8e-214       2     477 .]       6     483 ..       5     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 698.7 bits;  conditional E-value: 1.8e-214
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                            h+i+G+ + g+s++  pv npat+e ++ va a   evdaav++a  +f+awa t+ ++rar+l ++ ++++
  NCBI__GCF_000022085.1:WP_015929170.1   6 DHFIGGRRLAGRSGRSAPVFNPATGEQTGAVALADGSEVDAAVTAAAAAFPAWARTPPLRRARILNKFLQIIE 78 
                                           79*********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                           ++ d +a +i+ae+Gk+l+dakG++ rG+ev+e+a + + ll+Ge++e+v ++vd +++rqplGvvaGitpfn
  NCBI__GCF_000022085.1:WP_015929170.1  79 DRIDSLAAVITAEHGKVLSDAKGEIQRGMEVIEFAVGAPQLLKGEVTENVGTRVDSHALRQPLGVVAGITPFN 151
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fp m+p+wmfp+a+acGn+fvlkpse++psa++ lae l+eaG+pdGv+nvvhGdkeavd ll+hp+v  vsf
  NCBI__GCF_000022085.1:WP_015929170.1 152 FPVMVPMWMFPVALACGNCFVLKPSERDPSASLLLAEWLKEAGLPDGVFNVVHGDKEAVDALLHHPKVAGVSF 224
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..k 291
                                           vGs+++++yiy t++a+gkr qal+Gaknhm+++pdad ++a+dal+gaa+G+aG+rcma+s+av vG+   +
  NCBI__GCF_000022085.1:WP_015929170.1 225 VGSTPIARYIYATATANGKRAQALGGAKNHMIIMPDADMDQAVDALMGAAYGSAGERCMAVSVAVPVGEKtaN 297
                                           ********************************************************************86559 PP

                             TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364
                                            lve++  +++ ++vg+g+d  +e+Gpl+t+q+ ++v  +ia+g+ eGa++l+dGr +k++Gye G f+G tl
  NCBI__GCF_000022085.1:WP_015929170.1 298 TLVERLIPKVRALKVGPGTDRDSEMGPLVTRQHLDKVRGYIAQGVSEGAKLLVDGRDLKLQGYETGFFIGGTL 370
                                           9************************************************************************ PP

                             TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437
                                           +++v p+m+iykeeifGpvl+v +a  +  a +line  +GnGtaift+dG aar+f hei+vG+vG+nvpip
  NCBI__GCF_000022085.1:WP_015929170.1 371 FDHVTPEMTIYKEEIFGPVLAVTRAPDYATAARLINEHEFGNGTAIFTRDGDAAREFAHEIQVGMVGINVPIP 443
                                           ************************************************************************* PP

                             TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           vp++f+sf+Gwk+slfGd+h++G +Gvrfytrlk++t+rw
  NCBI__GCF_000022085.1:WP_015929170.1 444 VPMAFHSFGGWKASLFGDHHMHGPEGVRFYTRLKAITTRW 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: 00:00:00.01
# Mc/sec: 16.75
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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