GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Limnohabitans curvus MWH-C5

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_108401521.1 B9Z44_RS01610 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_003063475.1:WP_108401521.1
          Length = 487

 Score =  385 bits (989), Expect = e-111
 Identities = 204/475 (42%), Positives = 281/475 (59%), Gaps = 3/475 (0%)

Query: 6   YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65
           YT     I+G W   +   ++ ++NPAT   +G +  AG   +  A+AAA     + R +
Sbjct: 7   YTSHGQFINGTWRAGSESASV-MINPATEISLGEMKPAGAEQVTEAIAAAYEARTSMRAL 65

Query: 66  PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125
            A  R+A +R+AA  + ERA+ +  L+  E GKP+ +A  E  ++A+ ++WFADE RRV+
Sbjct: 66  TAWNRSALLRRAATFINERAEMLGHLVALETGKPIRQAVGEAKASAESVDWFADEARRVF 125

Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185
           G     R    +  V  EP+G VAAF PWNFP+  + RK++ ALA G + +++   E   
Sbjct: 126 GMSYESRVKSDRYLVHMEPLGVVAAFVPWNFPLLLLARKMAPALAAGNTLVIRPSSEAAG 185

Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245
           S  AL++ F DAG P GV+ LV G PAEI+  ++    + KV+FTGS P+G+Q+   + +
Sbjct: 186 STMALIKCFEDAGFPKGVVNLVIGRPAEITPTIMNDSRVAKVSFTGSVPIGRQIVEQSAI 245

Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305
            +KR +MELGGHAPVIV  DAD+      A   KFRNAGQVC SPTRF VH SI  E   
Sbjct: 246 TLKRVSMELGGHAPVIVHSDADIDAFAAMAAPGKFRNAGQVCASPTRFYVHESIAKEVEE 305

Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGG--ERIGSEG 363
            L+     L+VG+ L++ T LG LA  RR  A+  ++DNA   GA + +GG   R    G
Sbjct: 306 KLITATRALRVGSPLDDATDLGPLATRRRRDAIEQLVDNAVSGGARVLSGGMRPRRMDRG 365

Query: 364 NFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFAN 423
            F+ PT +  +  DA V N+EPFGP+  +  F  L++ IAEANRLPF LA Y FTRS   
Sbjct: 366 YFYEPTWLTQLQPDALVLNDEPFGPIGTLATFSTLDQVIAEANRLPFALAAYVFTRSLTK 425

Query: 424 VHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
            H    RL+ G++ +N       E PFGG KDSG+G EGGP A+  YL TK V V
Sbjct: 426 THATVDRLQAGVIGVNTFVAATAETPFGGSKDSGFGREGGPHAIRDYLDTKFVNV 480


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: 619
Number of extensions: 22
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: 481
Length of database: 487
Length adjustment: 34
Effective length of query: 447
Effective length of database: 453
Effective search space:   202491
Effective search space used:   202491
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: 52 (24.6 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