GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS00120
          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 (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