Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28030 BPHYT_RS28030 methylmalonate-semialdehyde dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS28030
          Length = 503

 Score =  847 bits (2188), Expect = 0.0
 Identities = 418/500 (83%), Positives = 457/500 (91%)

Query: 9   DTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISAAHRAFQTW 68
           +  V  VKLLI+G++VESKTTEW DI+NPATQ+VLA+VPFATA+EV+ AI +AH AF+TW
Sbjct: 4   NAAVATVKLLINGEFVESKTTEWRDIVNPATQEVLARVPFATADEVNEAIRSAHAAFKTW 63

Query: 69  KLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACSIGS 128
           K TPIGARMRIMLK QALIREHS RIA  LSAEQGKTI DAEGDIFRGLEVVEHACSIG+
Sbjct: 64  KDTPIGARMRIMLKYQALIREHSPRIARTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGT 123

Query: 129 LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQ 188
           LQ GEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAI CGNTFVLKPSEQ
Sbjct: 124 LQQGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQ 183

Query: 189 DPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAVGTHVYDLA 248
           DP+STM LVELA+EAG+P GVLNVVHGGK+VVD LCTH+ +KAVSFVGSTAVGTHVY L 
Sbjct: 184 DPLSTMQLVELALEAGVPKGVLNVVHGGKEVVDALCTHELVKAVSFVGSTAVGTHVYRLG 243

Query: 249 GKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWL 308
            +HGKRVQSMMGAKNHAVVLPDANREQ LNAL GAGFGAAGQRCMATSVVVLVGAA+QWL
Sbjct: 244 SEHGKRVQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMATSVVVLVGAAQQWL 303

Query: 309 PDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDGREISVPGY 368
           PDL A A+ LKVNAG+EP TD+GPV+S+ AK RIL LIE+G+KEGA L LDGR+I VPGY
Sbjct: 304 PDLVAKARTLKVNAGNEPNTDIGPVVSRAAKQRILGLIEAGVKEGATLALDGRDIKVPGY 363

Query: 369 EKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGNGTGLFTQS 428
           E+GNF+GPT+FS VTT+M+IY QEIFGPVLVVL   TLD+AIALVN NPFGNG GLFTQS
Sbjct: 364 EQGNFIGPTVFSDVTTEMEIYRQEIFGPVLVVLNAATLDDAIALVNRNPFGNGVGLFTQS 423

Query: 429 GAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 488
           GAAARKFQ+EID+GQVGINIPIPVPVP FSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT
Sbjct: 424 GAAARKFQSEIDIGQVGINIPIPVPVPSFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 483

Query: 489 SRWFDDDSVNDGVNTTINLR 508
           +RWFDDD+VNDGVNTTI+LR
Sbjct: 484 ARWFDDDTVNDGVNTTISLR 503


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: 842
Number of extensions: 28
Number of successful extensions: 2
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: 503
Length adjustment: 34
Effective length of query: 474
Effective length of database: 469
Effective search space:   222306
Effective search space used:   222306
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 BPHYT_RS28030 BPHYT_RS28030 (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.13309.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.7e-227  739.9   1.3   6.5e-227  739.8   1.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS28030  BPHYT_RS28030 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS28030  BPHYT_RS28030 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  739.8   1.3  6.5e-227  6.5e-227       1     477 []      10     486 ..      10     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 739.8 bits;  conditional E-value: 6.5e-227
                                TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                              vk+li+G+fve+k++++ ++ npat+evla+v++a+a+ev++a+ sa+ +f +w++t++  r r++l+yq
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030  10 VKLLINGEFVESKTTEWRDIVNPATQEVLARVPFATADEVNEAIRSAHAAFKTWKDTPIGARMRIMLKYQ 79 
                                              899******************************************************************* PP

                                TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvv 140
                                              al++eh   ia+ +saeqGkt+ da+Gd++rGlevvehacs+ +l +Ge  e+va  vd+y++rqp+Gv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030  80 ALIREHSPRIARTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGTLQQGEFAENVAGGVDTYTLRQPIGVC 149
                                              ********************************************************************** PP

                                TIGR01722 141 aGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrll 210
                                              aGitpfnfpamiplwmfp+ai+cGntfvlkpse++p+++++l el +eaG+p+GvlnvvhG+ke vd l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030 150 AGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPLSTMQLVELALEAGVPKGVLNVVHGGKEVVDALC 219
                                              ********************************************************************** PP

                                TIGR01722 211 ehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcma 280
                                               h  vkavsfvGs+avg ++y+ gs hgkrvq+++Gaknh+vvlpda++e++l+al ga +GaaGqrcma
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030 220 THELVKAVSFVGSTAVGTHVYRLGSEHGKRVQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMA 289
                                              ********************************************************************** PP

                                TIGR01722 281 isaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgyk 350
                                               s++vlvGaa++++++++ +a+ ++v+ag++p++++Gp+++++ak+r+  li++g+keGa + ldGr +k
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030 290 TSVVVLVGAAQQWLPDLVAKARTLKVNAGNEPNTDIGPVVSRAAKQRILGLIEAGVKEGATLALDGRDIK 359
                                              ********************************************************************** PP

                                TIGR01722 351 veGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaark 420
                                              v Gye+Gnf+G+t++++v ++m+iy++eifGpvlvvl+a tl++ai+l+n +p+GnG  +ft++Gaaark
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030 360 VPGYEQGNFIGPTVFSDVTTEMEIYRQEIFGPVLVVLNAATLDDAIALVNRNPFGNGVGLFTQSGAAARK 429
                                              ********************************************************************** PP

                                TIGR01722 421 fqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                              fq ei++GqvG+n+pipvp+p fsftG+++s  Gdl  yGkq v+fyt++ktvtarw
  lcl|FitnessBrowser__BFirm:BPHYT_RS28030 430 FQSEIDIGQVGINIPIPVPVPSFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARW 486
                                              ********************************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (503 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: 10.93
//
[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