GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Dechlorosoma suillum PS

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate Dsui_1464 Dsui_1464 NAD-dependent aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>FitnessBrowser__PS:Dsui_1464
          Length = 506

 Score =  773 bits (1997), Expect = 0.0
 Identities = 375/492 (76%), Positives = 422/492 (85%)

Query: 17  FEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGA 76
           ++ RYDNFIGG+WVAPV G+YF   TPITG    Q A+S A DIELALDAAHAA +KWG 
Sbjct: 15  YKARYDNFIGGKWVAPVKGQYFDVITPITGKPYTQAAQSGAEDIELALDAAHAAADKWGK 74

Query: 77  TSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRA 136
           TS  ER+NI+LKIADR+E NLE+LA  ET DNGK IRET+ AD+PLA DHFRYFAG LR+
Sbjct: 75  TSATERSNILLKIADRIEANLEMLAYVETVDNGKAIRETLNADIPLAADHFRYFAGCLRS 134

Query: 137 QEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTP 196
           QEGSIS+ID++T+AYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+ AGNCVVLKPAE TP
Sbjct: 135 QEGSISEIDENTIAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAESTP 194

Query: 197 AGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASE 256
             I+V A LI DLLPPGVLNIVNG+G +AG  LASS RIAKIAFTG T TGR+I Q A+ 
Sbjct: 195 ISILVLAELIADLLPPGVLNIVNGYGRDAGMALASSKRIAKIAFTGSTATGRVIAQAAAN 254

Query: 257 NLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIY 316
           +LIP TLELGGKSPNIFFADVA  DDDFFDKA+EG  +FA NQGEVCTCPSR LI ESIY
Sbjct: 255 SLIPATLELGGKSPNIFFADVAAADDDFFDKAIEGLVLFAFNQGEVCTCPSRALIHESIY 314

Query: 317 DKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAAD 376
           D FMER + RV+AIKQG P ++D+M+GAQAS  Q +KI+SYL IGK+EGA+ L GG  A 
Sbjct: 315 DHFMERVLARVKAIKQGSPLDTDSMMGAQASQMQMDKIMSYLAIGKEEGAQCLVGGDRAR 374

Query: 377 LGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGV 436
           LGGEL+ GYYI+PT+F+G+NKMRIFQEEIFGPV++VTTFK +AEALEIANDT YGLGAGV
Sbjct: 375 LGGELAEGYYIQPTLFKGHNKMRIFQEEIFGPVLAVTTFKTEAEALEIANDTPYGLGAGV 434

Query: 437 WSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNM 496
           WSRD NT YRMGRGIKAGRVWTNCYHAYPAHA FGGYK+SGIGRETHKMMLDHYQQTKN+
Sbjct: 435 WSRDGNTAYRMGRGIKAGRVWTNCYHAYPAHATFGGYKESGIGRETHKMMLDHYQQTKNL 494

Query: 497 LVSYSPKKLGFF 508
           LVSYSPK LGFF
Sbjct: 495 LVSYSPKALGFF 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: 859
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