GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Rhodobacter viridis JA737

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_110805439.1 C8J30_RS08590 betaine-aldehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>NCBI__GCF_003217355.1:WP_110805439.1
          Length = 483

 Score =  299 bits (765), Expect = 2e-85
 Identities = 183/476 (38%), Positives = 262/476 (55%), Gaps = 11/476 (2%)

Query: 12  NFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAE 71
           +F+NG WV+  +G  ++V  P    +++  +  +T   +E A+  A  A+ AW  L   E
Sbjct: 9   HFVNGNWVEDAAGAEIEVIFPG-TGEVIAILHEATPAVIEEALAGAQAAQRAWAALKPVE 67

Query: 72  RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAK-GETARGIAILRYYAGEGMRKTGDV 130
           R + L + AD++  R  E+A   T + GK + E    +   G   L Y+AG     TG+ 
Sbjct: 68  RARILRRAADLIRARRAELALLETLDTGKPIQETSVADWPSGADSLEYFAGLAPTLTGET 127

Query: 131 IPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCA 190
           IP     A  +T R PLGV   I  WN+P  I  WK APAL  GN ++ KP+  T +   
Sbjct: 128 IPLGGDFA--YTIREPLGVCVGIGAWNYPSQIACWKAAPALSTGNAMIFKPSEITPLGAL 185

Query: 191 KIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGA 250
           ++ A F EAG+PAGV N+V G G+V G+ LA    V  V+ TGS   G  +  AA A   
Sbjct: 186 QLAAIFVEAGMPAGVFNVVQGRGAVGGR-LATDSRVAKVSLTGSVPTGAKVYAAAGAGMK 244

Query: 251 KYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKLL 310
              +E+GGK+P+IV +DADLE+A  A + G F S+GQ C+  +RV V   I ERF  +L 
Sbjct: 245 HVTMELGGKSPLIVFEDADLESAIGAAMLGNFYSSGQICSNGTRVFVHKAIKERFLTRLA 304

Query: 311 QRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNGY 370
           +RT  I  GD L E    GP+ S  Q    L YI   K EGA L+ GG     G      
Sbjct: 305 ERTAAIKAGDPLDETTQFGPLVSAAQHAKVLGYIATAKSEGARLVCGGAAGAEG----AL 360

Query: 371 YVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGRM 430
           +VQP +F +VT  MTIA+EE+FGPV+A++  ++ +E +  AN   FGL+A +FT ++ R 
Sbjct: 361 FVQPTVFADVTDSMTIAREEVFGPVMAVLDFETEDEVIARANGTDFGLAAGVFTADLARG 420

Query: 431 LSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFV 486
              I ++ AG   INA +    ++ PFG +K SS   RE  +AA + +T +K V+V
Sbjct: 421 HRVIAQLQAGTTWINAYNL-TPVEMPFGAVK-SSGVGRENSKAAIEHYTQVKAVYV 474


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: 540
Number of extensions: 25
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: 483
Length adjustment: 34
Effective length of query: 454
Effective length of database: 449
Effective search space:   203846
Effective search space used:   203846
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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