Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E2

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Pf6N2E2_3452 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452
          Length = 508

 Score =  959 bits (2480), Expect = 0.0
 Identities = 476/508 (93%), Positives = 503/508 (99%)

Query: 1   MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA 60
           MNVSLTP+DTT+Q V+LLIDG+WVES+++EWHDI+NPATQQVLAKVPFATA EVDAAI+A
Sbjct: 1   MNVSLTPSDTTLQTVRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAA 60

Query: 61  AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120
           A RAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV
Sbjct: 61  AQRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120

Query: 121 EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180
           EHACSIG+LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT
Sbjct: 121 EHACSIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180

Query: 181 FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV 240
           FVLKPSEQDP+STMLLVELAIEAG+PAGVLNVVHGGKDVVD LCTHKDIKAVSFVGSTAV
Sbjct: 181 FVLKPSEQDPLSTMLLVELAIEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAV 240

Query: 241 GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300
           GTHVYDLAG+HGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL
Sbjct: 241 GTHVYDLAGRHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300

Query: 301 VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG 360
           VGAAKQWLP+LKALAQKLKVNAGSEPGTDVGPVISK+AKARIL+LIESG+++GAKLELDG
Sbjct: 301 VGAAKQWLPELKALAQKLKVNAGSEPGTDVGPVISKRAKARILELIESGVQQGAKLELDG 360

Query: 361 REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN 420
           R ISVPG+E+GNFVGPTLFSGVTTDM+IYT+EIFGPVLVVLEV+TLD+AIALVNANPFGN
Sbjct: 361 RGISVPGFEQGNFVGPTLFSGVTTDMRIYTEEIFGPVLVVLEVDTLDQAIALVNANPFGN 420

Query: 421 GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480
           GTGLFTQSGAAARKFQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF
Sbjct: 421 GTGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480

Query: 481 YTQTKTVTSRWFDDDSVNDGVNTTINLR 508
           YTQTKTVT+RWFDDDSVNDGVNTTINLR
Sbjct: 481 YTQTKTVTARWFDDDSVNDGVNTTINLR 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: 921
Number of extensions: 25
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 Pf6N2E2_3452 (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.1873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     4e-233  760.2   2.2   4.6e-233  760.1   2.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452  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 !  760.1   2.2  4.6e-233  4.6e-233       1     477 []      15     491 ..      15     491 .. 1.00

  Alignments for each domain:
  == domain 1  score: 760.1 bits;  conditional E-value: 4.6e-233
                                      TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerar 64 
                                                    v++lidG+ ve++s+++ ++ npat++vlakv++a+a evdaa+a+a+++f++w+ t++  r r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452  15 VRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAAAQRAFQTWKLTPIGARMR 78 
                                                    799************************************************************* PP

                                      TIGR01722  65 vllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdv 128
                                                    ++l+ qal++eh + ia ++saeqGkt++da+Gd++rGlevvehacs+ +l +Ge  e+va  v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452  79 IMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACSIGTLQMGEFAENVAGGV 142
                                                    **************************************************************** PP

                                      TIGR01722 129 dvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGap 192
                                                    d+y++rqp+Gv+aGitpfnfpamiplwmfp+aiacGntfvlkpse++p++++ l el  eaG+p
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452 143 DTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPLSTMLLVELAIEAGVP 206
                                                    **************************************************************** PP

                                      TIGR01722 193 dGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpd 256
                                                     GvlnvvhG+k+ vd l+ h d+kavsfvGs+avg ++y+ + +hgkrvq+++Gaknh+vvlpd
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452 207 AGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGRHGKRVQSMMGAKNHAVVLPD 270
                                                    **************************************************************** PP

                                      TIGR01722 257 adkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgaelGpli 320
                                                    a++e+al+alvga +GaaGqrcma s++vlvGaak++++e++  a+k++v+ag++pg+++Gp+i
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452 271 ANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPELKALAQKLKVNAGSEPGTDVGPVI 334
                                                    **************************************************************** PP

                                      TIGR01722 321 tkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvl 384
                                                    +k+ak+r+ +li+sg+++Ga++ ldGrg+ v G+e+GnfvG+tl+++v +dm+iy eeifGpvl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452 335 SKRAKARILELIESGVQQGAKLELDGRGISVPGFEQGNFVGPTLFSGVTTDMRIYTEEIFGPVL 398
                                                    **************************************************************** PP

                                      TIGR01722 385 vvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGw 448
                                                    vvle+dtl++ai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+pffsftG+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452 399 VVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGS 462
                                                    **************************************************************** PP

                                      TIGR01722 449 kdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                    ++s  Gdl  yGkq v+fyt++ktvtarw
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452 463 RGSKLGDLGPYGKQVVQFYTQTKTVTARW 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: 00:00:00.02
# Mc/sec: 8.28
//
[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)
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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