GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28150 BPHYT_RS28150 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__BFirm:BPHYT_RS28150
          Length = 505

 Score =  599 bits (1544), Expect = e-176
 Identities = 293/493 (59%), Positives = 368/493 (74%), Gaps = 3/493 (0%)

Query: 4   IKHLIGGELIAD-TGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           + H I G   A  +GR  DVF+P+ G    +VP+A+   +  A+ AAKAAFPAW  T P 
Sbjct: 12  LSHFIDGRRAAGASGRFGDVFDPAQGRVAARVPVANATEVDAAVAAAKAAFPAWSETAPL 71

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           KRA+++FRFK+LLEA+ + + +LI+ +HGK + DA GE+ RGIE VE+A   P +LK ++
Sbjct: 72  KRARLMFRFKELLEAHSDELAELITRDHGKLLSDAKGEVVRGIEIVEFACGIPNLLKTDF 131

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           +  +   ID W+  QP+GV AG+TPFNFP +VP WM+ +A ACGNTF+LKPSER PS+++
Sbjct: 132 TDQISGGIDNWNLRQPLGVAAGVTPFNFPMVVPCWMFVMAAACGNTFVLKPSERTPSASI 191

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242
            +AELF EAG PKGV NVVHG K  VDALIE P+V A+S VGSTP+AEYIYSE  KRGKR
Sbjct: 192 RLAELFIEAGFPKGVFNVVHGGKAVVDALIEHPDVAAISVVGSTPVAEYIYSESAKRGKR 251

Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302
           VQALG AKNH V+MPDADLD AV AL+ ++YGS GERCMA SVAV VG +I D L+++L 
Sbjct: 252 VQALGSAKNHLVVMPDADLDQAVDALIASSYGSAGERCMATSVAVAVG-RIGDELIERLA 310

Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGF 362
           P+++ L+IG G    LDMGPL++ A R KV GYID GVA GA LVVDGRG+ V GHE GF
Sbjct: 311 PRVRSLRIGGGMEPDLDMGPLISAAHRAKVLGYIDAGVAAGARLVVDGRGHSVPGHEAGF 370

Query: 363 FLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAA 422
           FLGG+LFD V P+M+IY+EEIFGPVL +VRV  L  A+ L+N HE GN   +FT DG AA
Sbjct: 371 FLGGSLFDDVKPDMSIYREEIFGPVLSVVRVPDLASAIALVNAHELGNCVSLFTSDGGAA 430

Query: 423 RLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWP 482
           R F  +I++GMVG+NVP PVP A+HSFGGWKRSLFGD HAYG + VRFYT  K++ QRWP
Sbjct: 431 RAFSRQIQIGMVGINVPSPVPPAWHSFGGWKRSLFGDHHAYGEEAVRFYTHYKSVMQRWP 490

Query: 483 QRKSHEAAQFAFP 495
              + + A+FA P
Sbjct: 491 DSIA-KGAEFAMP 502


Lambda     K      H
   0.319    0.137    0.411 

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: 737
Number of extensions: 27
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: 498
Length of database: 505
Length adjustment: 34
Effective length of query: 464
Effective length of database: 471
Effective search space:   218544
Effective search space used:   218544
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)

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:

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:

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:

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:

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