Alignments for a candidate for mmsA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas simiae WCS417

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF2142 PS417_10925 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__WCS417:GFF2142
          Length = 499

 Score =  594 bits (1532), Expect = e-174
 Identities = 285/499 (57%), Positives = 376/499 (75%), Gaps = 4/499 (0%)

Query: 2   TTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPP 61
           TTI H IN Q V+ + R Q+VFNPATGE   ++ LAS +TV +A++AAQ AF  W +TPP
Sbjct: 3   TTIEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPP 62

Query: 62  LKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGE 121
           ++RARV+F +  LL +  D++ R+I  EHGK+  DA GE+ RGI+ +E+ACG P LLKGE
Sbjct: 63  IRRARVLFEYLHLLRERKDDLARIIVAEHGKVFTDAQGEVDRGIDILEFACGIPNLLKGE 122

Query: 122 HSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSST 181
           HS  V  G+D+W+  QP+GVVAG+TPFNFPVMVP+WM+P+AI  GN F+LKPS  DPS++
Sbjct: 123 HSDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSAS 182

Query: 182 LYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGK 241
           L++A+LL+EAGLP GV NVV GDKE+VDAL+    VKAVSFVGSTPIA+YIY T + NGK
Sbjct: 183 LFMAELLREAGLPKGVFNVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYIYETGARNGK 242

Query: 242 RCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKM 301
           R Q LGGAKNH +VMPDAD++  V+ L+GAA+GS+GERCMA+SVAV VGD  GD +++ +
Sbjct: 243 RVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGD-VGDKVIAAL 301

Query: 302 TQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQ--PKVPNHE 359
           T+  + L++    D   + GP+++R   E++ GYI    Q GA +++DGR   P  P  E
Sbjct: 302 TERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPGLE 361

Query: 360 NGFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDG 419
           NGF++G TL DHVT EM+ Y+EEIFGPVL  VRV    +A+ L++AHE+GNG   FTRDG
Sbjct: 362 NGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDG 421

Query: 420 EAARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQ 479
             AR F+  I+VGMVGIN+P+ VP+A+H FGGWK+SLFGD+HAYG + VRFYTK+K++ Q
Sbjct: 422 NIAREFARRIEVGMVGINVPISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFYTKQKSIMQ 481

Query: 480 RWPSAGVREGAEFSMPTMK 498
           RW S  + +GAEF+MP  K
Sbjct: 482 RW-SESIEQGAEFAMPVSK 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: 694
Number of extensions: 28
Number of successful extensions: 4
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 GFF2142 PS417_10925 (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.11474.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.1e-207  674.2   0.1   5.8e-207  674.0   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF2142  PS417_10925 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2142  PS417_10925 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.0   0.1  5.8e-207  5.8e-207       2     477 .]       6     483 ..       5     483 .. 0.98

  Alignments for each domain:
  == domain 1  score: 674.0 bits;  conditional E-value: 5.8e-207
                           TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkeh 76 
                                         +h+i+ + v ++ d+y +v npat+e +++va as + v +ava+a+ +fa wa+t+  +rarvl+ y  ll+e+
  lcl|FitnessBrowser__WCS417:GFF2142   6 EHYINDQRV-SRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRARVLFEYLHLLRER 79 
                                         677777766.6889************************************************************* PP

                           TIGR01722  77 rdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpam 151
                                         +d++a++i+ae+Gk+++da+G+v rG++++e+ac+++ ll+Ge +++v++ +d +++rqplGvvaG+tpfnfp m
  lcl|FitnessBrowser__WCS417:GFF2142  80 KDDLARIIVAEHGKVFTDAQGEVDRGIDILEFACGIPNLLKGEHSDQVSRGMDNWTMRQPLGVVAGVTPFNFPVM 154
                                         *************************************************************************** PP

                           TIGR01722 152 iplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvav 226
                                         +p+wm+p+aia Gntf+lkps  +psa++ +aell+eaG+p+Gv+nvv Gdke+vd l+ehpdvkavsfvGs+++
  lcl|FitnessBrowser__WCS417:GFF2142 155 VPMWMYPIAIAAGNTFILKPSPTDPSASLFMAELLREAGLPKGVFNVVQGDKESVDALIEHPDVKAVSFVGSTPI 229
                                         *************************************************************************** PP

                           TIGR01722 227 geyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeirer 300
                                         ++yiyetg+++gkrvq l+Gaknhmvv+pdad e+++dal+gaa+G+aG+rcmais+avlvG++ ++++  + er
  lcl|FitnessBrowser__WCS417:GFF2142 230 AQYIYETGARNGKRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVgDKVIAALTER 304
                                         ****************************************************************9********** PP

                           TIGR01722 301 aekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgy..kveGyeeGnfvGitllervkpdmk 373
                                         a+ +r++ g d  ae+Gp+++++a er++ +i++g++ Ga++lldGr y  +  G e+G ++G tl+++v  +m+
  lcl|FitnessBrowser__WCS417:GFF2142 305 AKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYvpTEPGLENGFWLGATLFDHVTEEMS 379
                                         ************************************************944457********************* PP

                           TIGR01722 374 iykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGw 448
                                         iy+eeifGpvl+ ++++ + eaikl+n+  +GnG + ft+dG  ar+f  +ievG+vG+nvpi vp++++ f+Gw
  lcl|FitnessBrowser__WCS417:GFF2142 380 IYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDGNIAREFARRIEVGMVGINVPISVPMAWHGFGGW 454
                                         *************************************************************************** PP

                           TIGR01722 449 kdslfGdlhiyGkqGvrfytrlktvtarw 477
                                         k+slfGd+h+yG +Gvrfyt++k +  rw
  lcl|FitnessBrowser__WCS417:GFF2142 455 KKSLFGDMHAYGTEGVRFYTKQKSIMQRW 483
                                         ****************************9 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: 00:00:00.02
# 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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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