GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas stutzeri RCH2

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::P42236
         (488 letters)



>FitnessBrowser__psRCH2:GFF882
          Length = 499

 Score =  324 bits (830), Expect = 5e-93
 Identities = 178/480 (37%), Positives = 276/480 (57%), Gaps = 6/480 (1%)

Query: 8   NTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKL 67
           ++Y  FI+ +WV  + G+ + + NPA+   I+  + N+TA DV+RAV AA  A   WR  
Sbjct: 15  SSYGLFIDNQWVSDEYGETLDIINPAN-GKILTNIPNATAADVDRAVQAAQRAFMTWRTT 73

Query: 68  TGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRK 126
           + AER   L K AD++E   +  A   T ++GK + E++  +    I   RY+AG  +R 
Sbjct: 74  SPAERANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGV-IRS 132

Query: 127 TGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETA 186
             D     D+  L      PLGVVG + PWNFP+ +  WK+APA+  GNTVVIKP+  T 
Sbjct: 133 QSDEAVMLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTP 192

Query: 187 VTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAAL 246
           VT  ++   F +  LPAGV+N+VTG G+ VGQ L +H  +  + FTGS +VG+++  AA 
Sbjct: 193 VTILELAKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVANAAA 251

Query: 247 ARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFK 306
            +     LE+GGK+  IV  DA+ + A E  +     + GQ C + +R+ V   IYERF 
Sbjct: 252 KKIIPATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFL 311

Query: 307 EKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKY 366
            +L  + + + +GD L  D  MG   SK+Q++  L Y++  KQEGA +LIGG +L    Y
Sbjct: 312 AELKHKFEAVRVGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGGRLTGANY 371

Query: 367 QNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTEN 426
             G+++QP I   V ++M +A EEIFGPV+ +I      E + +AND ++GL+ +++T++
Sbjct: 372 DAGFFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQD 431

Query: 427 IGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFV 486
           I R L     ++ G + +N     +   APFGG K+S    RE  ++  + ++  K ++V
Sbjct: 432 INRALRVARAVETGRMWVNTYHE-IPAHAPFGGYKKSGL-GRETHKSMLEAYSQKKNIYV 489


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: 509
Number of extensions: 21
Number of successful extensions: 4
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: 499
Length adjustment: 34
Effective length of query: 454
Effective length of database: 465
Effective search space:   211110
Effective search space used:   211110
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