Alignments for a candidate for mmsA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens GW456-L13

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate PfGW456L13_5146 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146
         (508 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146
          Length = 508

 Score = 1006 bits (2602), Expect = 0.0
 Identities = 508/508 (100%), Positives = 508/508 (100%)

Query: 1   MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA 60
           MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA
Sbjct: 1   MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA 60

Query: 61  AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120
           AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV
Sbjct: 61  AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120

Query: 121 EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180
           EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT
Sbjct: 121 EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180

Query: 181 FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV 240
           FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV
Sbjct: 181 FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV 240

Query: 241 GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300
           GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL
Sbjct: 241 GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300

Query: 301 VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG 360
           VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG
Sbjct: 301 VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG 360

Query: 361 REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN 420
           REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN
Sbjct: 361 REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN 420

Query: 421 GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480
           GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF
Sbjct: 421 GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480

Query: 481 YTQTKTVTSRWFDDDSVNDGVNTTINLR 508
           YTQTKTVTSRWFDDDSVNDGVNTTINLR
Sbjct: 481 YTQTKTVTSRWFDDDSVNDGVNTTINLR 508


Lambda     K      H
   0.318    0.135    0.395 

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: 951
Number of extensions: 24
Number of successful extensions: 1
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: 508
Length of database: 508
Length adjustment: 34
Effective length of query: 474
Effective length of database: 474
Effective search space:   224676
Effective search space used:   224676
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate PfGW456L13_5146 (Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27))
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.15683.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   6.6e-232  756.2   2.4   7.5e-232  756.1   2.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146  Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  756.1   2.4  7.5e-232  7.5e-232       1     477 []      15     491 ..      15     491 .. 1.00

  Alignments for each domain:
  == domain 1  score: 756.1 bits;  conditional E-value: 7.5e-232
                                               TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawa 55 
                                                             vk+lidG+ ve+k++++ ++ npat++vlakv++a+aeevdaa+++a+++f++w+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146  15 VKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISAAHRAFQTWK 69 
                                                             899**************************************************** PP

                                               TIGR01722  56 etsvaerarvllryqallkehrdeiaklisaeqGktledakGdvarGlevvehac 110
                                                              t++  r r++l+ qal++eh + ia ++saeqGkt++da+Gd++rGlevvehac
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146  70 LTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHAC 124
                                                             ******************************************************* PP

                                               TIGR01722 111 svtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwmfplaiacGn 165
                                                             s+ sl +Ge  e+va  vd+y++rqp+Gv+aGitpfnfpamiplwmfp+aiacGn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 125 SIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGN 179
                                                             ******************************************************* PP

                                               TIGR01722 166 tfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                                             tfvlkpse++p +++ l el  eaG+p GvlnvvhG+k+ vd l+ h d+kavsf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 180 TFVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSF 234
                                                             ******************************************************* PP

                                               TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaG 275
                                                             vGs+avg ++y+ + +hgkrvq+++Gaknh+vvlpda++e+al+alvga +GaaG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 235 VGSTAVGTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAG 289
                                                             ******************************************************* PP

                                               TIGR01722 276 qrcmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervas 330
                                                             qrcma s++vlvGaak+++++++  a+k++v+ag++pg+++Gp+i+k+ak+r+ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 290 QRCMATSVVVLVGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILD 344
                                                             ******************************************************* PP

                                               TIGR01722 331 liasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlv 385
                                                             li+sg+keGa++ ldGr + v Gye+GnfvG+tl+++v +dm+iy +eifGpvlv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 345 LIESGIKEGAKLELDGREISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLV 399
                                                             ******************************************************* PP

                                               TIGR01722 386 vleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvpl 440
                                                             vle++tl+eai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 400 VLEVNTLDEAIALVNANPFGNGTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPV 454
                                                             ******************************************************* PP

                                               TIGR01722 441 pffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                             pffsftG+++s  Gdl  yGkq v+fyt++ktvt+rw
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 455 PFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTSRW 491
                                                             ************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (508 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: 6.40
//
[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
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