GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Burkholderia phytofirmans PsJN

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate BPHYT_RS00120 BPHYT_RS00120 aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS00120 BPHYT_RS00120 aldehyde
           dehydrogenase
          Length = 506

 Score =  792 bits (2045), Expect = 0.0
 Identities = 384/493 (77%), Positives = 425/493 (86%)

Query: 16  PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75
           P++++Y NFIGGEWV PV G YF N +PITG     I RS   D+ELALDAAH AK  WG
Sbjct: 14  PYKKQYANFIGGEWVKPVGGEYFDNVSPITGEAFTSIPRSREADVELALDAAHRAKAAWG 73

Query: 76  ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135
            TS  +R+NI+++IADRME NL+ LA AET DNGKP+RETMAAD+PLAIDHFRYFAG +R
Sbjct: 74  KTSAGDRSNILMRIADRMEANLQRLAVAETIDNGKPLRETMAADIPLAIDHFRYFAGAVR 133

Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195
           AQEGSIS+ID DTVAYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+AAGNCVVLKPAEQT
Sbjct: 134 AQEGSISEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQT 193

Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255
           PA I+V   LI DLLP GVLN+VNGFGLEAGKPLASS RIAKIAFTGETTTGRLIMQYAS
Sbjct: 194 PASILVLVELIQDLLPAGVLNVVNGFGLEAGKPLASSKRIAKIAFTGETTTGRLIMQYAS 253

Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315
           +N+IPVTLELGGKSPNIFF DV   DD +FDKALEGF MFALNQGEVCTCPSRVLI E I
Sbjct: 254 QNIIPVTLELGGKSPNIFFDDVMNADDSYFDKALEGFAMFALNQGEVCTCPSRVLIDEKI 313

Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375
           YD+FMERA++RV AI QG P ++ TMIGAQAS EQ EKILSY+D+GK+EGAE L GG+  
Sbjct: 314 YDRFMERALKRVAAITQGHPLDTRTMIGAQASQEQLEKILSYVDLGKQEGAECLIGGERN 373

Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435
            L GELS GYY++PT+FRG+NKMRIFQEEIFGPVVSVTTFK + EALE+ANDTLYGLGAG
Sbjct: 374 ALDGELSKGYYVKPTVFRGHNKMRIFQEEIFGPVVSVTTFKTEEEALEVANDTLYGLGAG 433

Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495
           VW+RD    YR GR I+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE HKMMLDHYQQTKN
Sbjct: 434 VWTRDGTRAYRFGRQIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493

Query: 496 MLVSYSPKKLGFF 508
           +LVSYS K LGFF
Sbjct: 494 LLVSYSDKPLGFF 506


Lambda     K      H
   0.319    0.136    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: 885
Number of extensions: 27
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: 508
Length of database: 506
Length adjustment: 34
Effective length of query: 474
Effective length of database: 472
Effective search space:   223728
Effective search space used:   223728
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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