Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Pf1N1B4_1229 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229
          Length = 505

 Score = 1001 bits (2588), Expect = 0.0
 Identities = 505/505 (100%), Positives = 505/505 (100%)

Query: 1   MNASLETTVQKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHR 60
           MNASLETTVQKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHR
Sbjct: 1   MNASLETTVQKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHR 60

Query: 61  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA 120
           AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA
Sbjct: 61  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA 120

Query: 121 CSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180
           CSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL
Sbjct: 121 CSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180

Query: 181 KPSEQDPMSTMLLVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 240
           KPSEQDPMSTMLLVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH
Sbjct: 181 KPSEQDPMSTMLLVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 240

Query: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGA 300
           VYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGA
Sbjct: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGA 300

Query: 301 AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDI 360
           AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDI
Sbjct: 301 AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDI 360

Query: 361 SVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 420
           SVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG
Sbjct: 361 SVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 420

Query: 421 LFTQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 480
           LFTQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ
Sbjct: 421 LFTQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 480

Query: 481 TKTVTARWFDDDSVNDGVNTTIHLR 505
           TKTVTARWFDDDSVNDGVNTTIHLR
Sbjct: 481 TKTVTARWFDDDSVNDGVNTTIHLR 505


Lambda     K      H
   0.319    0.135    0.397 

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: 964
Number of extensions: 26
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: 505
Length of database: 505
Length adjustment: 34
Effective length of query: 471
Effective length of database: 471
Effective search space:   221841
Effective search space used:   221841
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 Pf1N1B4_1229 (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.14195.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.1e-231  755.5   2.0   1.3e-231  755.3   2.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229  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 !  755.3   2.0  1.3e-231  1.3e-231       1     477 []      12     488 ..      12     488 .. 1.00

  Alignments for each domain:
  == domain 1  score: 755.3 bits;  conditional E-value: 1.3e-231
                                      TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerar 64 
                                                    vk+lidG+ ve++++++ ++ npat++vlakv++a+a+evdaa+++a+++f++w+ t++  r r
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229  12 VKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARMR 75 
                                                    899************************************************************* PP

                                      TIGR01722  65 vllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdv 128
                                                    ++l+ qal++eh + ia ++s eqGkt++da+Gd++rGlevvehacs+ sl +Ge  e+va  v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229  76 IMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFAENVAGGV 139
                                                    **************************************************************** PP

                                      TIGR01722 129 dvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGap 192
                                                    d+y++rqp+Gv+aGitpfnfpamiplwmfp+aiacGntfvlkpse++p +++ l el  eaG+p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229 140 DTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLLVELAIEAGIP 203
                                                    **************************************************************** PP

                                      TIGR01722 193 dGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpd 256
                                                     GvlnvvhG+k+ vd l+ h d+kavsfvGs+avg ++y+ + +hgkrvq+++Gaknh+vvlpd
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229 204 PGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRVQSMMGAKNHAVVLPD 267
                                                    **************************************************************** PP

                                      TIGR01722 257 adkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgaelGpli 320
                                                    a++e+al+alvga +GaaGqrcma s++vlvGaak+++++++  a+k++v+ag++pg+++Gp+i
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229 268 ANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVI 331
                                                    **************************************************************** PP

                                      TIGR01722 321 tkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvl 384
                                                    +k+ak+r+ +li+sg+keGa++ ldGr + v Gye+GnfvG+tl+++v p+m+iy +eifGpvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229 332 SKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVL 395
                                                    **************************************************************** PP

                                      TIGR01722 385 vvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGw 448
                                                    vvle+dtl++ai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+pffsftG+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229 396 VVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGS 459
                                                    **************************************************************** PP

                                      TIGR01722 449 kdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                    ++s  Gdl  yGkq v+fyt++ktvtarw
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229 460 RGSKLGDLGPYGKQVVQFYTQTKTVTARW 488
                                                    ***************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (505 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.56
//
[ok]

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

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Candidates (tab-delimited)
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