Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E3

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO353_21350 AO353_21350 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21350
          Length = 500

 Score =  623 bits (1606), Expect = 0.0
 Identities = 304/496 (61%), Positives = 384/496 (77%), Gaps = 3/496 (0%)

Query: 4   IGHLINGQLV-TENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPL 62
           IGH +NGQ+  T + R  NVFNPATG I  ++ LAS +TV++A+++A  AFP W     L
Sbjct: 7   IGHYLNGQVQDTGSERFSNVFNPATGAIQARVGLASQQTVDEAVASALRAFPAWSEQSSL 66

Query: 63  KRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEH 122
           +R+RVMF+FKELL++H +E+  +I  EHGK+  DA GE+ RGIE VEYACGAP LLK E 
Sbjct: 67  RRSRVMFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTEF 126

Query: 123 SRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTL 182
           S N+G GID+W+  QP+GV AG+TPFNFPVMVPLWM P+A+V GNCF+LKPSERDPS++L
Sbjct: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASL 186

Query: 183 YIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKR 242
            +A+LL EAGLPDGV +VV GDK AVDALL    ++A+SFVGSTPIAEYI++ A+A GKR
Sbjct: 187 LMARLLTEAGLPDGVFSVVQGDKSAVDALLQHPDIEAISFVGSTPIAEYIHQQATARGKR 246

Query: 243 CQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMT 302
            QALGGAKNH IVMPDAD+D A + L+GAAFGS+GERCMA+S+AVAVGD  GD L++K+ 
Sbjct: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAFGSAGERCMAISIAVAVGD-VGDKLIAKLL 305

Query: 303 QAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENGF 362
             + +LKVG      +D GP++T +H+ KV G+I+    QGA ++VDGR  KVP  ENGF
Sbjct: 306 PRIDQLKVGNGMQGDSDMGPLVTAEHKAKVEGFIDQGVAQGAQLIVDGRGFKVPGAENGF 365

Query: 363 FVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEAA 422
           FVG TL D VT EM+ YQ+EIFGPVL +VRVA    A+ LI+AHE+GNG   FT DG  A
Sbjct: 366 FVGATLFDKVTTEMSIYQQEIFGPVLGIVRVADFASAVALINAHEFGNGVSCFTSDGGIA 425

Query: 423 RYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRWP 482
           R F+  I+VGMVGIN+P+PVP+A+HSFGGWKRSLFGD HAYG + +RFY++ K+V QRWP
Sbjct: 426 RAFARTIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYSRYKSVMQRWP 485

Query: 483 SAGVREGAEFSMPTMK 498
            + + +G EFSMPT K
Sbjct: 486 DS-IAKGPEFSMPTAK 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: 726
Number of extensions: 24
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 AO353_21350 AO353_21350 (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.21927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.4e-211  689.2   0.2   1.7e-211  689.0   0.2    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350  AO353_21350 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350  AO353_21350 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.0   0.2  1.7e-211  1.7e-211       2     477 .]       8     484 ..       7     484 .. 1.00

  Alignments for each domain:
  == domain 1  score: 689.0 bits;  conditional E-value: 1.7e-211
                                     TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvl 66 
                                                    h+++G++ ++ s+++ +v npat+ + a+v  as++ vd+avasa ++f+aw+e s ++r+rv+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350   8 GHYLNGQVQDTGSERFSNVFNPATGAIQARVGLASQQTVDEAVASALRAFPAWSEQSSLRRSRVM 72 
                                                   599************************************************************** PP

                                     TIGR01722  67 lryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvy 131
                                                   +++++ll+ h++e+a++is e+Gk+++dakG+v rG+e+ve+ac+ + ll+ e ++++   +d +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350  73 FKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTEFSDNIGGGIDNW 137
                                                   ***************************************************************** PP

                                     TIGR01722 132 sirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvl 196
                                                    +rqplGv+aG+tpfnfp m+plwm pla++ Gn+f+lkpse++psa++ +a+ll+eaG+pdGv+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 138 NLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASLLMARLLTEAGLPDGVF 202
                                                   ***************************************************************** PP

                                     TIGR01722 197 nvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkea 261
                                                    vv Gdk avd ll+hpd+ a+sfvGs++++eyi+++++a+gkrvqal+Gaknhm+v+pdad+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 203 SVVQGDKSAVDALLQHPDIEAISFVGSTPIAEYIHQQATARGKRVQALGGAKNHMIVMPDADLDQ 267
                                                   ***************************************************************** PP

                                     TIGR01722 262 aldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqak 325
                                                   a+dal+gaa+G+aG+rcmais+av+vG++ ++l+ ++  r+++++vg g +  +++Gpl+t ++k
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 268 AADALIGAAFGSAGERCMAISIAVAVGDVgDKLIAKLLPRIDQLKVGNGMQGDSDMGPLVTAEHK 332
                                                   *****************************9*********************************** PP

                                     TIGR01722 326 ervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390
                                                   ++v+ +i++g+++Ga++++dGrg+kv G e+G fvG tl+++v ++m+iy++eifGpvl ++++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 333 AKVEGFIDQGVAQGAQLIVDGRGFKVPGAENGFFVGATLFDKVTTEMSIYQQEIFGPVLGIVRVA 397
                                                   ***************************************************************** PP

                                     TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455
                                                    +  a++lin+  +GnG + ftsdG+ ar f  +i+vG+vG+nvpipvp++++sf+Gwk slfGd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 398 DFASAVALINAHEFGNGVSCFTSDGGIARAFARTIKVGMVGINVPIPVPMAWHSFGGWKRSLFGD 462
                                                   ***************************************************************** PP

                                     TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477
                                                   +h+yG++G+rfy+r k v  rw
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 463 HHAYGEEGIRFYSRYKSVMQRW 484
                                                   *********************9 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.64
//
[ok]

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

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

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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 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