Alignments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_01202 H281DRAFT_01202 methylmalonate-semialdehyde dehydrogenase [acylating]

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



>FitnessBrowser__Burk376:H281DRAFT_01202
          Length = 502

 Score =  845 bits (2184), Expect = 0.0
 Identities = 416/494 (84%), Positives = 454/494 (91%)

Query: 14  VKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAAHRAFQTWKLTPIG 73
           VKLLI+G++V+S+TTEW D+VNPATQQVLA+VPFAT  EVD AI +AH AF+TWK TPIG
Sbjct: 9   VKLLINGEFVDSRTTEWRDVVNPATQQVLARVPFATAGEVDEAIRSAHAAFKTWKDTPIG 68

Query: 74  ARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEF 133
           ARMRIMLK QALIREH  RIA  LSAEQGKTI DAEGDIFRGLEVVEHACSIGSLQ GEF
Sbjct: 69  ARMRIMLKYQALIREHMPRIAKTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGSLQQGEF 128

Query: 134 AENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTM 193
           AENVAGGVDTYTLRQP+GVCAGITPFNFPAMIPLWMFPMAI CGNTFVLKPSEQDPMSTM
Sbjct: 129 AENVAGGVDTYTLRQPLGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPMSTM 188

Query: 194 LLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 253
            LVELA+EAG+P GVLNVVHGGKDVVDALCTH+ +KAVSFVGSTAVGTHVY L  +HGKR
Sbjct: 189 QLVELALEAGVPKGVLNVVHGGKDVVDALCTHELVKAVSFVGSTAVGTHVYRLGSEHGKR 248

Query: 254 VQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKAL 313
           VQSMMGAKNHAVVLPDANREQ LNAL GAGFGAAGQRCMATSVVVLVGAA+QWLP++ A 
Sbjct: 249 VQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMATSVVVLVGAAQQWLPEIVAK 308

Query: 314 AQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDITVPGYEKGNFV 373
           A+ LKVNAG+EP TD+GPV+S+ AK RIL LIE+G+KEGA L LDGRD+TVPGYE+GNF+
Sbjct: 309 AKTLKVNAGNEPNTDIGPVVSRAAKERILGLIEAGVKEGATLALDGRDVTVPGYEQGNFI 368

Query: 374 GPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARK 433
           GPT+FS V+T+M+IY  EIFGPVL+VL   TLD AIALVN+NPFGNG GLFTQSGAAARK
Sbjct: 369 GPTIFSDVSTEMEIYRTEIFGPVLLVLNAATLDDAIALVNSNPFGNGVGLFTQSGAAARK 428

Query: 434 FQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTSRWFDD 493
           FQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT+RWFDD
Sbjct: 429 FQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDD 488

Query: 494 DSVNDGVNTTINLR 507
           D+VNDGVNTTI+LR
Sbjct: 489 DTVNDGVNTTISLR 502


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: 830
Number of extensions: 23
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: 502
Length adjustment: 34
Effective length of query: 473
Effective length of database: 468
Effective search space:   221364
Effective search space used:   221364
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 H281DRAFT_01202 H281DRAFT_01202 (methylmalonate-semialdehyde dehydrogenase [acylating])
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.2087670.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.2e-227  740.8   1.6   3.6e-227  740.6   1.6    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01202  H281DRAFT_01202 methylmalonate-s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01202  H281DRAFT_01202 methylmalonate-semialdehyde dehydrogenase [acylating]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  740.6   1.6  3.6e-227  3.6e-227       1     477 []       9     485 ..       9     485 .. 1.00

  Alignments for each domain:
  == domain 1  score: 740.6 bits;  conditional E-value: 3.6e-227
                                    TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvl 66 
                                                  vk+li+G+fv+++++++ +v npat++vla+v++a+a evd+a+ sa+ +f +w++t++  r r++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202   9 VKLLINGEFVDSRTTEWRDVVNPATQQVLARVPFATAGEVDEAIRSAHAAFKTWKDTPIGARMRIM 74 
                                                  899*************************************************************** PP

                                    TIGR01722  67 lryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvys 132
                                                  l+yqal++eh   iak +saeqGkt+ da+Gd++rGlevvehacs+ sl +Ge  e+va  vd+y+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202  75 LKYQALIREHMPRIAKTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGSLQQGEFAENVAGGVDTYT 140
                                                  ****************************************************************** PP

                                    TIGR01722 133 irqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnv 198
                                                  +rqplGv+aGitpfnfpamiplwmfp+ai+cGntfvlkpse++p ++++l el +eaG+p+Gvlnv
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202 141 LRQPLGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPMSTMQLVELALEAGVPKGVLNV 206
                                                  ****************************************************************** PP

                                    TIGR01722 199 vhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaald 264
                                                  vhG+k+ vd l+ h  vkavsfvGs+avg ++y+ gs hgkrvq+++Gaknh+vvlpda++e++l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202 207 VHGGKDVVDALCTHELVKAVSFVGSTAVGTHVYRLGSEHGKRVQSMMGAKNHAVVLPDANREQTLN 272
                                                  ****************************************************************** PP

                                    TIGR01722 265 alvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervas 330
                                                  al ga +GaaGqrcma s++vlvGaa+++++ei+ +a+ ++v+ag++p++++Gp+++++aker+  
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202 273 ALAGAGFGAAGQRCMATSVVVLVGAAQQWLPEIVAKAKTLKVNAGNEPNTDIGPVVSRAAKERILG 338
                                                  ****************************************************************** PP

                                    TIGR01722 331 liasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeai 396
                                                  li++g+keGa + ldGr ++v Gye+Gnf+G+t++++v ++m+iy+ eifGpvl vl+a tl++ai
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202 339 LIEAGVKEGATLALDGRDVTVPGYEQGNFIGPTIFSDVSTEMEIYRTEIFGPVLLVLNAATLDDAI 404
                                                  ****************************************************************** PP

                                    TIGR01722 397 klinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkq 462
                                                  +l+n +p+GnG  +ft++Gaaarkfq ei+vGqvG+n+pipvp+pffsftG+++s  Gdl  yGkq
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202 405 ALVNSNPFGNGVGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQ 470
                                                  ****************************************************************** PP

                                    TIGR01722 463 Gvrfytrlktvtarw 477
                                                   v+fyt++ktvtarw
  lcl|FitnessBrowser__Burk376:H281DRAFT_01202 471 VVQFYTQTKTVTARW 485
                                                  *************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (502 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.11
//
[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