GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Geotalea uraniireducens Rf4

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_011940134.1 GURA_RS16875 aldehyde dehydrogenase family protein

Query= SwissProt::P42236
         (488 letters)



>NCBI__GCF_000016745.1:WP_011940134.1
          Length = 496

 Score =  384 bits (985), Expect = e-111
 Identities = 199/476 (41%), Positives = 280/476 (58%), Gaps = 2/476 (0%)

Query: 12  NFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAE 71
           NFI G W+    G      NPAD  + +  V  S   DV+RAV AA EA   WR +    
Sbjct: 7   NFIGGAWIPPAGGKRFASVNPADNRETIAEVSLSERGDVDRAVAAAREAFRTWRLMPPPR 66

Query: 72  RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGDVI 131
           RG+ L++ A+++  R  E+    TREMGK L E  G+    I +  Y AGEG R  G+ +
Sbjct: 67  RGEILFRAAELLAGRKAELGELVTREMGKVLAEGLGDVQEAIDMAYYMAGEGRRWQGETV 126

Query: 132 PSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCAK 191
           PS   D    + R PLGVV +++PWNFP AIP WK+ PAL+ GNTV+ KP++ T    A 
Sbjct: 127 PSELPDKDCKSVRQPLGVVALVTPWNFPTAIPAWKLFPALICGNTVIFKPSSATPACAAA 186

Query: 192 IIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGAK 251
           I+    EAG+P GV+NLV GPG  +G+ L  H GV+A +FTGS   G+ +          
Sbjct: 187 IVETLSEAGIPPGVVNLVHGPGEEIGEYLLTHPGVDAASFTGSCAAGERLEGLLGKMHRP 246

Query: 252 YQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKLLQ 311
             LEMGGKN VIV  DADL  A E V+ G F ++GQ+CT+ SRVIV   +Y+RF E L++
Sbjct: 247 LALEMGGKNAVIVMADADLSLALEGVLWGGFGTSGQRCTSASRVIVNEQVYDRFVEMLVE 306

Query: 312 RTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNGYY 371
             K + +G+ L ++  +GP+ ++ Q    L YI  G  EG  LL GG ++  G   NG++
Sbjct: 307 GAKRLRLGNGLHKETDVGPLINEQQCRKVLDYIRIGIGEGGELLTGGRQVTEGGCGNGWF 366

Query: 372 VQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGRML 431
           ++P +F  V  EM IA+EEIFGPV+++IK     EA+ IANDV  GLS++I++ ++    
Sbjct: 367 IEPTVFGGVRPEMRIAREEIFGPVVSVIKCGGFAEAVEIANDVPMGLSSAIYSRDVNLTA 426

Query: 432 SFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQG--EAAKDFFTAIKTVF 485
               ++ +G+V INA + G E+  PFGG K S S   E G    A DF++ +K ++
Sbjct: 427 RAERDLQSGIVYINASTIGAEIHLPFGGWKHSGSGHPEAGGRGGALDFYSRVKVIY 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: 588
Number of extensions: 20
Number of successful extensions: 2
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: 496
Length adjustment: 34
Effective length of query: 454
Effective length of database: 462
Effective search space:   209748
Effective search space used:   209748
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 Apr 09 2024. 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