GapMind for catabolism of small carbon sources

 

Alignments 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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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