GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Phaeobacter inhibens BS107

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Phaeo:GFF2135
          Length = 485

 Score =  348 bits (892), Expect = e-100
 Identities = 190/475 (40%), Positives = 287/475 (60%), Gaps = 8/475 (1%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FINGEY +  +G     +    G  +A V +   A   +A+  A+A   +  W+++   +
Sbjct: 12  FINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKA--WARMTGTE 69

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L R AD++R+   +L++LET D GKP+ ++   D    A A+ +       +  E 
Sbjct: 70  RGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEH 129

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
            P   D +    RE +G+   I  WN+P  +ACWK  PALA GNS+V KPSE +PL A++
Sbjct: 130 IPLGEDWV-YTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALK 188

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           +A++ IEAG PAGV NV+ G G  VG AL     VD +  TGS    K++   A E  MK
Sbjct: 189 VAEILIEAGAPAGVFNVVQGMGE-VGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEG-MK 246

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322
            + +E GGKSP I+F DA D+  A   A +   ++ G+VC+ G+R+ V++ IK+KFL  +
Sbjct: 247 HVTMELGGKSPLIIFDDA-DIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARL 305

Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTY 382
            E       G+P+D  T+ G +V   QMN VL YIE G ++GA+L+ GG+R   +  G +
Sbjct: 306 AERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRA--DMDGYF 363

Query: 383 VEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAH 442
           +EPT+F  VT+ M IA+EEIFGPV+SV+ FDT EE VA ANDT +GL+AG++T D ++AH
Sbjct: 364 IEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAH 423

Query: 443 KTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           +    + AGS ++N Y+   + APFGG K SG GR+ S  A++ ++++K+ ++++
Sbjct: 424 RVIGNLEAGSCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVRM 478


Lambda     K      H
   0.316    0.132    0.390 

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: 589
Number of extensions: 27
Number of successful extensions: 6
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: 497
Length of database: 485
Length adjustment: 34
Effective length of query: 463
Effective length of database: 451
Effective search space:   208813
Effective search space used:   208813
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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