GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Phaeobacter inhibens BS107

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB

Query= SwissProt::P42236
         (488 letters)



>FitnessBrowser__Phaeo:GFF2135
          Length = 485

 Score =  325 bits (834), Expect = 2e-93
 Identities = 189/478 (39%), Positives = 285/478 (59%), Gaps = 13/478 (2%)

Query: 12  NFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAE 71
           +FINGE+V+  +G  + V   A   + +  V  +T   VE+A++ A  A+ AW ++TG E
Sbjct: 11  HFINGEYVEDTAGTPIPVIYAA-TGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTE 69

Query: 72  RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAK-GETARGIAILRYYAGEGMRKTGDV 130
           RG+ L + ADIM +R  +++   T + GK L E    +   G   L Y+ G     TG+ 
Sbjct: 70  RGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEH 129

Query: 131 IPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCA 190
           IP  +    ++T R  LG+   I  WN+P  I  WK APAL  GN++V KP+  T +   
Sbjct: 130 IPLGED--WVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCAL 187

Query: 191 KIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGA 250
           K+     EAG PAGV N+V G G V G  L     V+ V+ TGS   GK +  AA A G 
Sbjct: 188 KVAEILIEAGAPAGVFNVVQGMGEV-GGALVTDPRVDKVSLTGSVPTGKKV-YAAAAEGM 245

Query: 251 KY-QLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKL 309
           K+  +E+GGK+P+I+ DDAD++ A    I G F S+GQ C+  +RV VQ GI E+F  +L
Sbjct: 246 KHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARL 305

Query: 310 LQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNG 369
            +RT +  +GD + E    GP+ ++NQ++  L YIEKGK+EGA L+ GG + +     +G
Sbjct: 306 AERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRAD----MDG 361

Query: 370 YYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGR 429
           Y+++P +F +VT +MTIA+EEIFGPV++++  D+ EE +  AND +FGLSA +FT++  R
Sbjct: 362 YFIEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTR 421

Query: 430 MLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFVK 487
               I  ++AG   IN+ +    ++APFGG+K +S   RE  + A   F+ +K+V+V+
Sbjct: 422 AHRVIGNLEAGSCFINSYN-DAPVEAPFGGVK-ASGVGRENSKEAIKHFSQVKSVYVR 477


Lambda     K      H
   0.315    0.132    0.374 

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: 562
Number of extensions: 28
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: 488
Length of database: 485
Length adjustment: 34
Effective length of query: 454
Effective length of database: 451
Effective search space:   204754
Effective search space used:   204754
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 (21.5 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