GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Dinoroseobacter shibae DFL-12

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 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__Dino:3609503
          Length = 492

 Score =  353 bits (907), Expect = e-102
 Identities = 192/463 (41%), Positives = 263/463 (56%), Gaps = 1/463 (0%)

Query: 15  GEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATM 74
           G W DA SG T  V NPA G  I  V   G A+  RA+AAA +  + W    A +RA  +
Sbjct: 26  GAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVL 85

Query: 75  RKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNL 134
           R+   L+   AD +A+++T E GKPL EAR EV+  A  +EWFA+E +R+YG  +P    
Sbjct: 86  RRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIPGHLP 145

Query: 135 GAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAF 194
            A+  V+++P+G V A TPWNFP+  + RK + ALA GC+FL K  E+TP S  AL    
Sbjct: 146 DARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALAVLA 205

Query: 195 VDAGVPAGVIGLV-YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATME 253
             AG+PAG+  ++   D + I      +  +RK+TFTGST VG+ L + A   +K+ +ME
Sbjct: 206 ERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKCSME 265

Query: 254 LGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEG 313
           LGG+AP IV +DAD+  AV+ A   KFRNAGQ C+   R  V + + D F   L    E 
Sbjct: 266 LGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAAAVEE 325

Query: 314 LKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIAN 373
           LKVG+G  EG T+G L N   +  +   +D+ R  G ++ TGGE     G FF PTV+  
Sbjct: 326 LKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTPTVVTG 385

Query: 374 VPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEV 433
           V  +  V   E FGPVA +  F + +E IA AN   FGLAGY + R    +  +++ LE 
Sbjct: 386 VTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSEALEY 445

Query: 434 GMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           G++ IN         PFGGVK SG G EG    ++ YL  K +
Sbjct: 446 GIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYI 488


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: 609
Number of extensions: 16
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: 492
Length adjustment: 34
Effective length of query: 447
Effective length of database: 458
Effective search space:   204726
Effective search space used:   204726
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 17 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