Aligments for a candidate for adh in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Cupriavidus basilensis 4G11

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate RR42_RS34255 RR42_RS34255 aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>FitnessBrowser__Cup4G11:RR42_RS34255
          Length = 506

 Score =  790 bits (2040), Expect = 0.0
 Identities = 379/495 (76%), Positives = 429/495 (86%)

Query: 14  ALPFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEK 73
           A P++E+Y+N+IGG W+AP  G+YF   +P+TG    ++ RS   D++ ALDAAH AK  
Sbjct: 12  AYPYKEQYENYIGGAWLAPADGQYFEAISPVTGKPFTRVPRSNQKDVDAALDAAHRAKGA 71

Query: 74  WGATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGV 133
           WG TS  ERANI+ +IADR+E NL  LA AET DNGKPIRET AADLPLA+DHFRYFAG 
Sbjct: 72  WGRTSTTERANILNRIADRIEANLVTLAVAETIDNGKPIRETTAADLPLAVDHFRYFAGC 131

Query: 134 LRAQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAE 193
           +RAQEG IS+ID DTVAYHFHEPLGVVGQIIPWNFPLLMA WKLAPA+AAGNCVVLKPAE
Sbjct: 132 IRAQEGGISEIDHDTVAYHFHEPLGVVGQIIPWNFPLLMATWKLAPALAAGNCVVLKPAE 191

Query: 194 QTPAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQY 253
           QTPA I+V   +IGDLLPPGVLN++NGFGLEAGKPLASS+RI+KIAFTGETTTGRLIMQY
Sbjct: 192 QTPASILVLMEIIGDLLPPGVLNVINGFGLEAGKPLASSSRISKIAFTGETTTGRLIMQY 251

Query: 254 ASENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQE 313
           AS+NLIPVTLELGGKSPNIFF DV   DD +FDKALEGF MFALNQGEVCTCPSR LIQE
Sbjct: 252 ASQNLIPVTLELGGKSPNIFFEDVLSADDAYFDKALEGFAMFALNQGEVCTCPSRALIQE 311

Query: 314 SIYDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGK 373
           SIY++FMERA++RV AIKQG P +  TMIGAQAS EQ EKILSY+D+GK+EGA+ L GG+
Sbjct: 312 SIYERFMERALKRVAAIKQGHPLDKATMIGAQASQEQLEKILSYIDLGKQEGAQCLIGGE 371

Query: 374 AADLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLG 433
              LGG+L+ GYY++PT+F G+NKMRIFQEEIFGPVVSVTTFKD+ EALEIANDTLYGLG
Sbjct: 372 RNALGGDLASGYYVKPTVFSGHNKMRIFQEEIFGPVVSVTTFKDEEEALEIANDTLYGLG 431

Query: 434 AGVWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQT 493
           AGVW+RD    +RMGRGI+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE H+MMLDHYQQT
Sbjct: 432 AGVWTRDGARAFRMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHRMMLDHYQQT 491

Query: 494 KNMLVSYSPKKLGFF 508
           KN+LVSYSP  LGFF
Sbjct: 492 KNLLVSYSPNALGFF 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: 24
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources