GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Acidovorax sp. GW101-3H11

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate Ac3H11_4393 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::psRCH2:GFF2231
         (506 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4393
          Length = 507

 Score =  763 bits (1969), Expect = 0.0
 Identities = 365/505 (72%), Positives = 426/505 (84%)

Query: 2   IYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKA 61
           +YA PG PGA +++KP+Y N+IGG+FVPPVKG+YF   +PV+G+V     RS AEDIE A
Sbjct: 3   VYAAPGAPGAKITYKPQYDNFIGGKFVPPVKGQYFDVITPVSGKVYTRAARSTAEDIELA 62

Query: 62  LDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLA 121
           LDAAHAAAD+WGKT    RA ILLKIA+RIE NLE+LA AET DNGKA+RETLNAD+PL 
Sbjct: 63  LDAAHAAADSWGKTDAATRANILLKIANRIEENLERLAYAETVDNGKAIRETLNADIPLT 122

Query: 122 ADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAA 181
            DHFRYFAGC+RAQEG+ + I+E+T AYH  EPLGVVGQIIPWNFP+LMAAWKLAPAL A
Sbjct: 123 VDHFRYFAGCVRAQEGALSNIDENTVAYHIQEPLGVVGQIIPWNFPILMAAWKLAPALGA 182

Query: 182 GNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTGS 241
           GNC+VLKPAE TP+SI++ +E++ DLLPPGVLNIV GFGREAG  LA S RIAKIAFTGS
Sbjct: 183 GNCVVLKPAESTPISILILVELIADLLPPGVLNIVNGFGREAGMPLAQSKRIAKIAFTGS 242

Query: 242 TPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVC 301
           T  G  I + AA N+IP+T+ELGGKSPNIFF DIM+ + AF++KA EGLVL  FNQGEVC
Sbjct: 243 TSTGRVIAQAAANNLIPATLELGGKSPNIFFADIMDKDDAFLDKAIEGLVLFAFNQGEVC 302

Query: 302 TCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQ 361
           TCPSRA+IQESI++ FME V+K++ AIK  NPLDTD+M+GAQAS++Q  KILSY+++ +Q
Sbjct: 303 TCPSRAIIQESIYDQFMERVLKRVAAIKHQNPLDTDSMMGAQASKEQLTKILSYLDLGKQ 362

Query: 362 EGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEALA 421
           EGA++L GG    L G L  GYYVQPTL KGHNKMR+FQEEIFGPV+ V TFKDEAEALA
Sbjct: 363 EGAEVLAGGGQAHLGGDLEGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEALA 422

Query: 422 IANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETH 481
           IANDT +GLGAGVW+R+ N AYRMGR IKAGRVWTNCYH YPAHAAFGGYK+SG+GRETH
Sbjct: 423 IANDTLYGLGAGVWSRNGNVAYRMGRAIKAGRVWTNCYHAYPAHAAFGGYKESGIGRETH 482

Query: 482 KMMLDHYQQTKNLLISYDINPLGFF 506
           KMMLDHYQQTKNLL+SY  N LGFF
Sbjct: 483 KMMLDHYQQTKNLLVSYSENKLGFF 507


Lambda     K      H
   0.319    0.136    0.406 

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: 760
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: 506
Length of database: 507
Length adjustment: 34
Effective length of query: 472
Effective length of database: 473
Effective search space:   223256
Effective search space used:   223256
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 (21.8 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