GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Porphyrobacter dokdonensis DSW-74

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_068863622.1 I603_RS07320 aldehyde dehydrogenase family protein

Query= SwissProt::A1B4L2
         (508 letters)



>NCBI__GCF_001677335.1:WP_068863622.1
          Length = 506

 Score =  788 bits (2036), Expect = 0.0
 Identities = 382/489 (78%), Positives = 424/489 (86%)

Query: 20  RYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGATSP 79
           +YDNFIGG+WVAPV  +YF N +P+ G  + Q+AR  A DIELALDAAH A+  WG TS 
Sbjct: 18  KYDNFIGGQWVAPVKCQYFDNISPVNGKRVCQVARGSAEDIELALDAAHKARAAWGRTST 77

Query: 80  AERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRAQEG 139
            ER+NI+ +IA R+E NL+LLA  ET DNGKPIRET AADLPLA+DHFRYFAG LRAQEG
Sbjct: 78  TERSNILNRIAQRIEDNLDLLALVETIDNGKPIRETTAADLPLAVDHFRYFAGALRAQEG 137

Query: 140 SISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTPAGI 199
            IS+ID DT+AYHFHEPLGVVGQIIPWNFPLLMA WKLAPA+AAGNCVVLKPAEQTP  I
Sbjct: 138 GISEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMAVWKLAPALAAGNCVVLKPAEQTPMSI 197

Query: 200 MVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASENLI 259
           MV   +IGDLLP GV+N+VNGFG+EAGKPLA+S RIAKIAFTGETTTGRLIMQYASENLI
Sbjct: 198 MVLMEVIGDLLPEGVVNVVNGFGIEAGKPLATSPRIAKIAFTGETTTGRLIMQYASENLI 257

Query: 260 PVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIYDKF 319
           P TLELGGKSPNIFFADV REDDD+ DKALEGF MFALNQGEVCTCPSR LI ESIYD+F
Sbjct: 258 PCTLELGGKSPNIFFADVMREDDDYLDKALEGFAMFALNQGEVCTCPSRALIHESIYDRF 317

Query: 320 MERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAADLGG 379
           ME+A+ RV AIK G P ++ TMIGAQAS++Q EKILSY++IGK EGA+VLTGG      G
Sbjct: 318 MEKAIARVNAIKLGSPLDAATMIGAQASNDQLEKILSYIEIGKGEGAKVLTGGGRHIHEG 377

Query: 380 ELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGVWSR 439
           EL+ GYY++PT+  G+NKMRIFQEEIFGPV+SVTTFKD  EAL IANDTLYGLGAGVWSR
Sbjct: 378 ELAEGYYVKPTVLEGHNKMRIFQEEIFGPVLSVTTFKDNDEALSIANDTLYGLGAGVWSR 437

Query: 440 DANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNMLVS 499
           DANTCYR GR I+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE HKMML+HYQQTKN+LVS
Sbjct: 438 DANTCYRFGRAIEAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLEHYQQTKNLLVS 497

Query: 500 YSPKKLGFF 508
           YSPK LGFF
Sbjct: 498 YSPKALGFF 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: 909
Number of extensions: 35
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 24 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