GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Snodgrassella alvi wkB2

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate WP_025330278.1 SALWKB2_RS03375 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_000600005.1:WP_025330278.1
          Length = 456

 Score =  232 bits (592), Expect = 2e-65
 Identities = 139/452 (30%), Positives = 239/452 (52%), Gaps = 6/452 (1%)

Query: 29  VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH--ERAATMRKAAALVRERAD 86
           +NP TG+     ++    +++  L  A + +++    P +  ER A +++ A ++    +
Sbjct: 6   INPFTGELARTFSNHTNTEVENVLTQAHALYKSEWSQPENISERQALLQRLAEIMTRHQE 65

Query: 87  AIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVKEPVG 146
            IA+++T + GK + E+R E+++  +I++++A +   +      P  LG +  V   P+G
Sbjct: 66  KIARIITLDMGKRIAESRNEIVNCIEIVQYYAKQAAELLKPAAYPSKLG-KGWVEHHPIG 124

Query: 147 PVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPAGVIGL 206
            + A  PWNFP+ Q++R ++ A+A G   + K     P     +     +A  PAG    
Sbjct: 125 IILAVEPWNFPIYQLIRVIAPAIAVGNPVVAKHASNVPQCAQLVEDLLHEAQAPAGTYTN 184

Query: 207 VYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVIVAEDA 266
           ++  P +I + +I    ++ V  TGS   G  +A  AG  +K++TMELGG+   +V +DA
Sbjct: 185 LFVTPEQIET-IIGDKRVQGVALTGSEGAGIIVAGQAGSKLKKSTMELGGNDVFVVTDDA 243

Query: 267 DVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGLEEGTTL 326
           DV  A   A   +  NAGQVCI+  RF+VH  + ++FTR + +    + +G+ L+E TTL
Sbjct: 244 DVVAAAHTAVAGRLFNAGQVCIAAKRFIVHEKVAEQFTRIVQEDFAQVVMGDPLDENTTL 303

Query: 327 GALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVFNNEPF 386
             L++ +    +   +D A   GA +  G +   ++GNFF PT+I ++  D   +  E F
Sbjct: 304 APLSSRKSKDTLQEQLDAAIAHGAKVICGNK--PAKGNFFTPTLITDISRDNPAYFEEFF 361

Query: 387 GPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQPATPWP 446
           GPVA +      EEAI  AN   FGL G  F++       L  R+E GM++IN+      
Sbjct: 362 GPVAQLYIVKNDEEAITLANDSNFGLGGTVFSKDIERAKKLASRIETGMVFINRFGDSVA 421

Query: 447 EMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
           E+PFGG+K SG+G E     ++ ++  K V +
Sbjct: 422 ELPFGGIKRSGFGRELSDLGIKEFVNHKLVVL 453


Lambda     K      H
   0.318    0.134    0.393 

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: 31
Number of successful extensions: 5
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: 481
Length of database: 456
Length adjustment: 33
Effective length of query: 448
Effective length of database: 423
Effective search space:   189504
Effective search space used:   189504
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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