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.20754.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  lcl|FitnessBrowser__psRCH2:GFF3712  Psest_3781 methylmalonic acid se


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3712  Psest_3781 methylmalonic acid semialdehyde dehydrogenase
   #    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 lidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                         li+ + v g+s+++  v npa++e    v+ +sa+e  +a+a+a+ +f  w++t+ + rarv++r+++ll+ +rd
  lcl|FitnessBrowser__psRCH2:GFF3712   7 LINNEAVAGRSERHATVYNPANGEPRLYVSLSSADETREAIAAAQAAFDGWSKTPPLVRARVMFRFKELLERRRD 81 
                                         789999********************************************************************* PP

                           TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamip 153
                                         ++a+li++e+Gk+++da+G+v rGlevve+ac+++ ll+Ge +++v +d+d  s+ qplGv++Gitpfnfpam+p
  lcl|FitnessBrowser__psRCH2:GFF3712  82 DVARLITSEHGKVFSDAQGEVTRGLEVVEFACGIPHLLKGEFSSNVGRDIDSNSLMQPLGVCVGITPFNFPAMVP 156
                                         *************************************************************************** PP

                           TIGR01722 154 lwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavge 228
                                         lwm+p+aiacGntfvlkpsek+psa++ l ell eaG+p Gvln+v Gdkeavd ll    v++vsfvGs++++e
  lcl|FitnessBrowser__psRCH2:GFF3712 157 LWMLPVAIACGNTFVLKPSEKDPSATMLLGELLAEAGLPAGVLNIVNGDKEAVDVLLTDERVQSVSFVGSTPIAE 231
                                         *************************************************************************** PP

                           TIGR01722 229 yiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeirera 301
                                         yiy t+sahgkr qal+Gaknhmvv+pdad ++++++l+gaa+G+aG+rcmais+av vG+   ++lv  +++ +
  lcl|FitnessBrowser__psRCH2:GFF3712 232 YIYATASAHGKRCQALGGAKNHMVVMPDADPQQVVSSLIGAAYGSAGERCMAISVAVCVGDEvaDKLVGMLQDEI 306
                                         ************************************************************7446*********** PP

                           TIGR01722 302 ekvrvgag..ddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmki 374
                                          ++r g+g   +p  ++Gpl+t++++++v+ +i+ g++eGa ++ dGrg+kveG+e+G +vG+tl++rv p+m+i
  lcl|FitnessBrowser__psRCH2:GFF3712 307 GQMRTGPGlgIEPEPHMGPLVTREHQQKVSGYIDLGVEEGATLVCDGRGIKVEGHENGFYVGPTLFDRVTPSMRI 381
                                         ****999633699************************************************************** PP

                           TIGR01722 375 ykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwk 449
                                         y+eeifGpvl+v+++ +++ea++lin+  yGnGt+ift+dG +ar+f+ +++vG+vGvnvpipvp++f+ f+Gwk
  lcl|FitnessBrowser__psRCH2:GFF3712 382 YREEIFGPVLAVVRVKSFDEALQLINDHEYGNGTSIFTRDGDTARQFEENVKVGMVGVNVPIPVPMAFHCFGGWK 456
                                         *************************************************************************** PP

                           TIGR01722 450 dslfGdlhiyGkqGvrfytrlktvtarw 477
                                          s+fG l+++G +Gvrf+tr+ktvt rw
  lcl|FitnessBrowser__psRCH2:GFF3712 457 RSVFGPLNMHGPDGVRFFTRMKTVTRRW 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.94
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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, or view the source code.

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