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 (EC 1.2.1.27) (characterized)
to candidate AO353_05990 AO353_05990 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_05990
         (507 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05990
          Length = 507

 Score = 1004 bits (2597), Expect = 0.0
 Identities = 507/507 (100%), Positives = 507/507 (100%)

Query: 1   MNASLTPETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAA 60
           MNASLTPETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAA
Sbjct: 1   MNASLTPETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAA 60

Query: 61  HRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVE 120
           HRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVE
Sbjct: 61  HRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVE 120

Query: 121 HACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTF 180
           HACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTF
Sbjct: 121 HACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTF 180

Query: 181 VLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVG 240
           VLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVG
Sbjct: 181 VLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVG 240

Query: 241 THVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLV 300
           THVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLV
Sbjct: 241 THVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLV 300

Query: 301 GAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGR 360
           GAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGR
Sbjct: 301 GAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGR 360

Query: 361 DITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNG 420
           DITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNG
Sbjct: 361 DITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNG 420

Query: 421 TGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFY 480
           TGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFY
Sbjct: 421 TGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFY 480

Query: 481 TQTKTVTSRWFDDDSVNDGVNTTINLR 507
           TQTKTVTSRWFDDDSVNDGVNTTINLR
Sbjct: 481 TQTKTVTSRWFDDDSVNDGVNTTINLR 507


Lambda     K      H
   0.319    0.135    0.396 

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: 981
Number of extensions: 28
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: 507
Length of database: 507
Length adjustment: 34
Effective length of query: 473
Effective length of database: 473
Effective search space:   223729
Effective search space used:   223729
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_05990 AO353_05990 (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.6324.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.7e-232  756.7   2.4   5.4e-232  756.5   2.4    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990  AO353_05990 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990  AO353_05990 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  756.5   2.4  5.4e-232  5.4e-232       1     477 []      14     490 ..      14     490 .. 1.00

  Alignments for each domain:
  == domain 1  score: 756.5 bits;  conditional E-value: 5.4e-232
                                     TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarv 65 
                                                   vk+lidG+ ve++++++ ++ npat++vlakv++a+ +evdaa+++a+++f++w+ t++  r r+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990  14 VKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAAHRAFQTWKLTPIGARMRI 78 
                                                   899************************************************************** PP

                                     TIGR01722  66 llryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdv 130
                                                   +l+ qal++eh + ia ++saeqGkt++da+Gd++rGlevvehacs+ sl +Ge  e+va  vd+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990  79 MLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFAENVAGGVDT 143
                                                   ***************************************************************** PP

                                     TIGR01722 131 ysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGv 195
                                                   y++rqp+Gv+aGitpfnfpamiplwmfp+aiacGntfvlkpse++p +++ l el  eaG+p Gv
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 144 YTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLLVELAIEAGIPAGV 208
                                                   ***************************************************************** PP

                                     TIGR01722 196 lnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadke 260
                                                   lnvvhG+k+ vd l+ h d+kavsfvGs+avg ++y+ + +hgkrvq+++Gaknh+vvlpda++e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 209 LNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANRE 273
                                                   ***************************************************************** PP

                                     TIGR01722 261 aaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqak 325
                                                   +al+alvga +GaaGqrcma s++vlvGaak+++++++  a+k++v+ag++pg+++Gp+i+k+ak
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 274 QALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAK 338
                                                   ***************************************************************** PP

                                     TIGR01722 326 ervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390
                                                   +r+ +li+sg+keGa++ ldGr ++v Gye+GnfvG+tl+++v +dm+iy +eifGpvlvvle+d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 339 ARILDLIESGIKEGAKLELDGRDITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVD 403
                                                   ***************************************************************** PP

                                     TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455
                                                   tl++ai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+pffsftG+++s  Gd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 404 TLDQAIALVNANPFGNGTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGD 468
                                                   ***************************************************************** PP

                                     TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477
                                                   l  yGkq v+fyt++ktvt+rw
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 469 LGPYGKQVVQFYTQTKTVTSRW 490
                                                   ********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (507 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: 11.48
//
[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