GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Dinoroseobacter shibae DFL-12

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= SwissProt::A1B4L2
         (508 letters)



>lcl|FitnessBrowser__Dino:3607686 Dshi_1095 aldehyde dehydrogenase
           (RefSeq)
          Length = 506

 Score =  791 bits (2043), Expect = 0.0
 Identities = 379/493 (76%), Positives = 427/493 (86%)

Query: 16  PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75
           PF++RYDNFIGG++V PV GRYF N TPITG  +GQIARS A D+ELALDAAHAAK+ WG
Sbjct: 14  PFKDRYDNFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDAWG 73

Query: 76  ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135
            TS  ERANI+LKIADR+E NL+++A AETWDNGKPIRET  AD+PLA+DHFRYFAGVLR
Sbjct: 74  KTSVTERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLR 133

Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195
            QEGS+S+ID+DTVAYHFHEPLGVVGQIIPWNF +LMA WKLAPAIAAGNC+VLKPAEQT
Sbjct: 134 GQEGSMSEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQT 193

Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255
           PA IMV   LI DLLP GVLNIVNG+G E G  LA+S+RIAKIAFTG T TGR IM+ A+
Sbjct: 194 PAAIMVLVELISDLLPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAAT 253

Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315
            NLIPVTLELGGKSPNIFF DV  EDD F DKA+EGF +FA NQGEVCTCPSR LI E I
Sbjct: 254 VNLIPVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAFNQGEVCTCPSRALIHEDI 313

Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375
           Y++F+ RA+ RV+AI QGDPR+ +TM+GAQAS EQK+KILSY  IG +EGAEVLTGGK A
Sbjct: 314 YEEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVA 373

Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435
           D+  +L  G+YIEPTI +G+NKMR+FQEEIFGPVVSVTTFK + EALE+ANDT+YGLGAG
Sbjct: 374 DVSDDLKDGFYIEPTILKGHNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAG 433

Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495
           VWSRD NTCYR GRG++AGRVW N YHAYPAHAAFGGYKQSGIGRE HKMMLDHYQQTKN
Sbjct: 434 VWSRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493

Query: 496 MLVSYSPKKLGFF 508
           MLVSY+P KLGFF
Sbjct: 494 MLVSYNPNKLGFF 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: 899
Number of extensions: 29
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.

Links

Downloads

Related tools

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