GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::A1B4L2
         (508 letters)



>FitnessBrowser__Cola:Echvi_0481
          Length = 509

 Score =  699 bits (1805), Expect = 0.0
 Identities = 333/504 (66%), Positives = 399/504 (79%)

Query: 5   QTHPFRGVNALPFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELAL 64
           Q  P   ++   F+  YDNFIGG++V PV G YF   +P+ G    ++AR +A DIELAL
Sbjct: 6   QEKPATMLDRPDFKPHYDNFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELAL 65

Query: 65  DAAHAAKEKWGATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAI 124
           DAAH A   W  TS  ER+NI+LKIADR+E  LE LA  ET DNGKP+RET+ ADL L +
Sbjct: 66  DAAHKAFPAWSRTSATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVV 125

Query: 125 DHFRYFAGVLRAQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAG 184
           DHFRYFAGV+RA+EGSI+++D  TV+ +  EP+G+VGQIIPWNFP+LMA WK+APA+AAG
Sbjct: 126 DHFRYFAGVIRAEEGSIAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAG 185

Query: 185 NCVVLKPAEQTPAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGET 244
            C ++KPAEQTPA IM+   +IGDLLP GVLN+VNGFG EAGKPLA S R+ K+AFTGET
Sbjct: 186 CCTIVKPAEQTPASIMILMEVIGDLLPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGET 245

Query: 245 TTGRLIMQYASENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCT 304
           TTGRLIMQYASENL PVT+ELGGKSPN+FF  V   DD+F DK LEG  MFALNQGEVCT
Sbjct: 246 TTGRLIMQYASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCT 305

Query: 305 CPSRVLIQESIYDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKE 364
           CPSR+L+ E IYD FME+ + R +AI+ G P +  TM+GAQAS +Q EKILSY+DIGK+E
Sbjct: 306 CPSRILVHEKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQE 365

Query: 365 GAEVLTGGKAADLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEI 424
           GAEVLTGG+ A L   L  GYY++PT+ +G+NKMR+FQEEIFGPV SV TFKD  EA+ I
Sbjct: 366 GAEVLTGGEVAKLNSGLENGYYVKPTLLKGHNKMRVFQEEIFGPVCSVATFKDVEEAISI 425

Query: 425 ANDTLYGLGAGVWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHK 484
           +NDTLYGLGAGVW+RDA+  Y++ R IKAGRVW NCYHAYPAHA FGGYK+SG GRETH 
Sbjct: 426 SNDTLYGLGAGVWTRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHL 485

Query: 485 MMLDHYQQTKNMLVSYSPKKLGFF 508
           MML+HY+Q KNML+SY   KLGFF
Sbjct: 486 MMLNHYRQNKNMLISYDKNKLGFF 509


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: 831
Number of extensions: 28
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: 509
Length adjustment: 34
Effective length of query: 474
Effective length of database: 475
Effective search space:   225150
Effective search space used:   225150
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