GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Halioglobus japonicus S1-36

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_084200632.1 C0029_RS01440 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_002869505.1:WP_084200632.1
          Length = 487

 Score =  654 bits (1688), Expect = 0.0
 Identities = 307/483 (63%), Positives = 394/483 (81%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           + L D  L + QAY++G WVDAD+G T  V NPATGE+I  + ++GAAET RAI AAD A
Sbjct: 3   LTLSDPTLLKHQAYINGEWVDADDGATFAVTNPATGEVITEIARVGAAETARAIAAADTA 62

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
           +  W+ + AK RA  LR+WFDLM+E+Q+DLA+LMT EQGK +AE++GEIAY A+F+EWFG
Sbjct: 63  MADWKKVPAKARAQVLRKWFDLMMEHQEDLAQLMTAEQGKVIAESRGEIAYGAAFIEWFG 122

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EEAKRI GD IPG   DKRI+ IKQP+GV AAITPWNFP+AMI RKA PALAAGC++V+K
Sbjct: 123 EEAKRIDGDVIPGPSSDKRIVCIKQPVGVVAAITPWNFPNAMIARKAAPALAAGCSIVIK 182

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240
           PAS+TP SALA+AELAERAG+P GV +VV GSA ++G E+TSNP VRKLTFTGST IG+ 
Sbjct: 183 PASETPLSALAMAELAERAGVPAGVVNVVAGSASKIGAEITSNPTVRKLTFTGSTPIGKM 242

Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300
           L+ +CA  +KK S+ELGGNAPFIVFDDAD+D+A+ GA+ISKYRN GQTCVC+NR++VQDG
Sbjct: 243 LVEQCAPTMKKTSMELGGNAPFIVFDDADIDSAITGAMISKYRNAGQTCVCSNRIFVQDG 302

Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360
           VYD FV K   A A+L +GNG + GV  GPL+  KA+  V++ + +++++GA+V +GG  
Sbjct: 303 VYDEFVAKFVKATAELTVGNGADDGVVIGPLVTEKAMNDVDKLVQESIAQGAQVAAGGSA 362

Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420
           H+LGG+F++PT+L +V  +  V ++E FGP++PV RF  E EVIAM+NDTEFGLASYFY 
Sbjct: 363 HSLGGSFYQPTVLTEVTSDMAVFRNEIFGPVSPVVRFSTEEEVIAMANDTEFGLASYFYT 422

Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           RD+ RV+R+AE L+YG+VGIN G+ISNE+APFGG+K SG GREGSKYGI+DY+EIKY+ +
Sbjct: 423 RDIGRVWRIAEALDYGIVGINEGIISNEMAPFGGVKESGSGREGSKYGIDDYVEIKYMLM 482

Query: 481 GGI 483
           GG+
Sbjct: 483 GGL 485


Lambda     K      H
   0.317    0.135    0.391 

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: 692
Number of extensions: 16
Number of successful extensions: 1
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: 483
Length of database: 487
Length adjustment: 34
Effective length of query: 449
Effective length of database: 453
Effective search space:   203397
Effective search space used:   203397
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