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 GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>FitnessBrowser__psRCH2:GFF2584
          Length = 490

 Score =  334 bits (857), Expect = 4e-96
 Identities = 182/477 (38%), Positives = 281/477 (58%), Gaps = 6/477 (1%)

Query: 13  FINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAER 72
           +I+G +V + S +  +  NPA+  +++  V  + A D+ERAV +A + +  W  LTG ER
Sbjct: 10  YIHGGYVDASSNETFESINPAN-GEVLAQVAEAGAADLERAVESAEQGQRIWAALTGIER 68

Query: 73  GQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRKTGDVI 131
            + + +  D++ +R +E+A   T + GK L E +  +   G  +L YYAG      G+ I
Sbjct: 69  ARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEGEQI 128

Query: 132 PSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCAK 191
           P  D  + ++T R PLGVV  I  WN+P+ I +WK APAL  GN ++ KP+  T+++  K
Sbjct: 129 PLRDS-SFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSALK 187

Query: 192 IIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGAK 251
           +   F EAGLP GV N++TG G+ VG  + EH  +  V+FTG    GK +  +A +   K
Sbjct: 188 LAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSSLK 247

Query: 252 -YQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKLL 310
              +E+GGK+P+I+ +DADL+ AA+  +   F S+GQ CT  +RV V +G+   F+ KLL
Sbjct: 248 DVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEAKLL 307

Query: 311 QRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNGY 370
           +R + I +GD  +E+   GP+ S   ++N L YI KGK  GA LL GGE++  G+Y  G 
Sbjct: 308 ERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEYAKGA 367

Query: 371 YVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGRM 430
           +V P IF + + +M I  EEIFGPV++L++    +E +  AND ++GL+A + T ++ R 
Sbjct: 368 FVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADLARA 427

Query: 431 LSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFVK 487
              I  ++AG+  IN        Q P GG KQS    RE G A+   +T +K+V V+
Sbjct: 428 HRIIHRLEAGICWINTWGES-PAQMPVGGYKQSGI-GRENGIASLAHYTRVKSVQVE 482


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: 564
Number of extensions: 24
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: 490
Length adjustment: 34
Effective length of query: 454
Effective length of database: 456
Effective search space:   207024
Effective search space used:   207024
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