Alignments for a candidate for mmsA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas stutzeri RCH2

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3712 Psest_3781 methylmalonic acid semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__psRCH2:GFF3712
          Length = 500

 Score =  635 bits (1638), Expect = 0.0
 Identities = 310/501 (61%), Positives = 383/501 (76%), Gaps = 4/501 (0%)

Query: 1   MTTIGHLINGQLVT-ENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNT 59
           M T+G+LIN + V   + R   V+NPA GE    + L+S     +AI+AAQ AF  W  T
Sbjct: 1   MQTLGNLINNEAVAGRSERHATVYNPANGEPRLYVSLSSADETREAIAAAQAAFDGWSKT 60

Query: 60  PPLKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLK 119
           PPL RARVMFRFKELLE+  D++ RLI  EHGK+  DA GE+ RG+E VE+ACG P LLK
Sbjct: 61  PPLVRARVMFRFKELLERRRDDVARLITSEHGKVFSDAQGEVTRGLEVVEFACGIPHLLK 120

Query: 120 GEHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPS 179
           GE S NVG  IDS S  QP+GV  GITPFNFP MVPLWM P+AI CGN FVLKPSE+DPS
Sbjct: 121 GEFSSNVGRDIDSNSLMQPLGVCVGITPFNFPAMVPLWMLPVAIACGNTFVLKPSEKDPS 180

Query: 180 STLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASAN 239
           +T+ + +LL EAGLP GV+N+VNGDKEAVD LL D+RV++VSFVGSTPIAEYIY TASA+
Sbjct: 181 ATMLLGELLAEAGLPAGVLNIVNGDKEAVDVLLTDERVQSVSFVGSTPIAEYIYATASAH 240

Query: 240 GKRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVS 299
           GKRCQALGGAKNH +VMPDAD    V+ L+GAA+GS+GERCMA+SVAV VGD   D LV 
Sbjct: 241 GKRCQALGGAKNHMVVMPDADPQQVVSSLIGAAYGSAGERCMAISVAVCVGDEVADKLVG 300

Query: 300 KMTQAMQKLKVGP--STDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPN 357
            +   + +++ GP    +     GP++TR+HQ+KV GYI+   ++GAT+V DGR  KV  
Sbjct: 301 MLQDEIGQMRTGPGLGIEPEPHMGPLVTREHQQKVSGYIDLGVEEGATLVCDGRGIKVEG 360

Query: 358 HENGFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTR 417
           HENGF+VG TL D VTP M  Y+EEIFGPVL VVRV +  +A+ LI+ HEYGNGT IFTR
Sbjct: 361 HENGFYVGPTLFDRVTPSMRIYREEIFGPVLAVVRVKSFDEALQLINDHEYGNGTSIFTR 420

Query: 418 DGEAARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTV 477
           DG+ AR F +N++VGMVG+N+P+PVP+A+H FGGWKRS+FG L+ +GPD VRF+T+ KTV
Sbjct: 421 DGDTARQFEENVKVGMVGVNVPIPVPMAFHCFGGWKRSVFGPLNMHGPDGVRFFTRMKTV 480

Query: 478 TQRWPSAGVREGAEFSMPTMK 498
           T+RWP+ G+R GAEF+MPTMK
Sbjct: 481 TRRWPT-GIRAGAEFAMPTMK 500


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: 761
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: 500
Length adjustment: 34
Effective length of query: 464
Effective length of database: 466
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate GFF3712 Psest_3781 (methylmalonic acid 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.583372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.1e-210  685.3   0.0   2.4e-210  685.1   0.0    1.0  1  FitnessBrowser__psRCH2:GFF3712  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__psRCH2:GFF3712  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.1   0.0  2.4e-210  2.4e-210       4     477 .]       7     484 ..       4     484 .. 0.99

  Alignments for each domain:
  == domain 1  score: 685.1 bits;  conditional E-value: 2.4e-210
                       TIGR01722   4 lidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrdeiak 82 
                                     li+ + v g+s+++  v npa++e    v+ +sa+e  +a+a+a+ +f  w++t+ + rarv++r+++ll+ +rd++a+
  FitnessBrowser__psRCH2:GFF3712   7 LINNEAVAGRSERHATVYNPANGEPRLYVSLSSADETREAIAAAQAAFDGWSKTPPLVRARVMFRFKELLERRRDDVAR 85 
                                     789999************************************************************************* PP

                       TIGR01722  83 lisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwmfplai 161
                                     li++e+Gk+++da+G+v rGlevve+ac+++ ll+Ge +++v +d+d  s+ qplGv++Gitpfnfpam+plwm+p+ai
  FitnessBrowser__psRCH2:GFF3712  86 LITSEHGKVFSDAQGEVTRGLEVVEFACGIPHLLKGEFSSNVGRDIDSNSLMQPLGVCVGITPFNFPAMVPLWMLPVAI 164
                                     ******************************************************************************* PP

                       TIGR01722 162 acGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkr 240
                                     acGntfvlkpsek+psa++ l ell eaG+p Gvln+v Gdkeavd ll    v++vsfvGs++++eyiy t+sahgkr
  FitnessBrowser__psRCH2:GFF3712 165 ACGNTFVLKPSEKDPSATMLLGELLAEAGLPAGVLNIVNGDKEAVDVLLTDERVQSVSFVGSTPIAEYIYATASAHGKR 243
                                     ******************************************************************************* PP

                       TIGR01722 241 vqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvgag..ddpgae 315
                                      qal+Gaknhmvv+pdad ++++++l+gaa+G+aG+rcmais+av vG+   ++lv  +++ + ++r g+g   +p  +
  FitnessBrowser__psRCH2:GFF3712 244 CQALGGAKNHMVVMPDADPQQVVSSLIGAAYGSAGERCMAISVAVCVGDEvaDKLVGMLQDEIGQMRTGPGlgIEPEPH 322
                                     ************************************************7446***************999633699*** PP

                       TIGR01722 316 lGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtlee 394
                                     +Gpl+t++++++v+ +i+ g++eGa ++ dGrg+kveG+e+G +vG+tl++rv p+m+iy+eeifGpvl+v+++ +++e
  FitnessBrowser__psRCH2:GFF3712 323 MGPLVTREHQQKVSGYIDLGVEEGATLVCDGRGIKVEGHENGFYVGPTLFDRVTPSMRIYREEIFGPVLAVVRVKSFDE 401
                                     ******************************************************************************* PP

                       TIGR01722 395 aiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktv 473
                                     a++lin+  yGnGt+ift+dG +ar+f+ +++vG+vGvnvpipvp++f+ f+Gwk s+fG l+++G +Gvrf+tr+ktv
  FitnessBrowser__psRCH2:GFF3712 402 ALQLINDHEYGNGTSIFTRDGDTARQFEENVKVGMVGVNVPIPVPMAFHCFGGWKRSVFGPLNMHGPDGVRFFTRMKTV 480
                                     ******************************************************************************* PP

                       TIGR01722 474 tarw 477
                                     t rw
  FitnessBrowser__psRCH2:GFF3712 481 TRRW 484
                                     **** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (500 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.48
//
[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