GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Thiomicrospira cyclica ALM1

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_013834856.1 THICY_RS01540 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_000214825.1:WP_013834856.1
          Length = 456

 Score =  233 bits (593), Expect = 1e-65
 Identities = 144/452 (31%), Positives = 232/452 (51%), Gaps = 4/452 (0%)

Query: 29  VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW-RKVPAHERAATMRKAAALVRERADA 87
           +NPATG+ +          LD A+  A + F  W ++     R   ++ A  ++R + D 
Sbjct: 6   INPATGEKLAEFEAWDQERLDLAIRRANAEFLEWSQRTSLATRCELIKNAGKILRAQQDE 65

Query: 88  IAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVKEPVGP 147
           +A+L+T E GK + EA+ E+  +A + +++A+ G +      P     ++  +  +P+G 
Sbjct: 66  LAKLITLEMGKSINEAKAEIEKSAWVCDFYAEHGPKFLAD-EPIATDASKSYICYQPLGL 124

Query: 148 VAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPAGVIGLV 207
           V A  PWNFP  QV R  + AL  G   L+K     P    A+ R F++AG+PA V   +
Sbjct: 125 VLAVMPWNFPFWQVFRFAAPALIAGNIGLLKHASNVPQCAQAIERIFIEAGLPASVFTNL 184

Query: 208 YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVIVAEDAD 267
                ++ S +I    +R VT TGS P G+++A++AG  +K+  +ELGG    IV  DAD
Sbjct: 185 MIGSDKVES-VIRSRYVRAVTLTGSEPAGRKVAAIAGEELKKTVLELGGSDAFIVMSDAD 243

Query: 268 VALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKV-GNGLEEGTTL 326
           +  AV+AA  +++ N GQ CI+  RF+V   I ++F   L    E   V G+ L+  TTL
Sbjct: 244 IPAAVEAAVTSRYLNMGQSCIAAKRFIVDTFIYEDFITRLKTAVESRFVEGDPLDPATTL 303

Query: 327 GALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVFNNEPF 386
             +A    L  +   +      GA + TGG ++   G ++APT++A++      ++ E F
Sbjct: 304 CPMARQDLLDELHQQVQTCVDYGARLVTGGYQLDRPGCYYAPTILADISSAMPAYHEEFF 363

Query: 387 GPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQPATPWP 446
           GPVA I    +   A+  AN   FGL G  ++   A    +  R+E G  ++N      P
Sbjct: 364 GPVALIFKASEPAHAVGLANATQFGLGGSVWSSDGATAETMALRMESGACFVNGMTKSDP 423

Query: 447 EMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
            +PFGGVK+SGYG E     +  +   KS+ +
Sbjct: 424 RLPFGGVKNSGYGRELSYHGIREFTNIKSIWI 455


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: 536
Number of extensions: 36
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 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