GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Dechlorosoma suillum PS

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= curated2:Q1QTQ7
         (489 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  214 bits (546), Expect = 4e-60
 Identities = 166/469 (35%), Positives = 230/469 (49%), Gaps = 16/469 (3%)

Query: 4   KQQLLIDGAWVDGDAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFA 63
           +QQ  ++G WV G++  F   +P SG  L       A +   A+AAA  A+P W  R+  
Sbjct: 10  RQQCYLNGQWVGGESD-FPVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSRTAK 68

Query: 64  ERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGER 123
           ER  V+ R+ E +  H + LA  +  E GKPL EAR EV      V           GE 
Sbjct: 69  ERTGVLRRWFELMNQHADDLALLMTSEQGKPLAEARGEVAYAASFVEWFAEEAKRAYGET 128

Query: 124 ARDIG-DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTAD 182
              +  D R ++  +P GV A   P+NFP  +    + PAL AG  VV KP+EQTP+TA 
Sbjct: 129 IPAVAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLTAL 188

Query: 183 LTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVD 241
              +    AG PAGV N++ G    +G  L  +  +  L FTGS +VG LL  Q    + 
Sbjct: 189 ALAELAHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPSIK 248

Query: 242 KILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDA 301
           K L+LELGGN P +V D  D +AAV   + S + + GQ C CA RL+V  G + +     
Sbjct: 249 K-LSLELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDG-IYEAFAAR 306

Query: 302 LTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLS---RMRRLQAG 358
           L + +A L+V    +E       L   +A   + A   D VA G R L+   R  R + G
Sbjct: 307 LAAKVATLKVGEG-TEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHERYREG 365

Query: 359 TSLLSPG-LIDVT-GCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGERA 416
            +   P  L DVT    V  EE FGP+  + R++  +EAIALAN T +GL++     +  
Sbjct: 366 GAFFQPTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSRDIG 425

Query: 417 DWDDFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSAYYAAD 463
                   +  G+V  N   TG  S+  APFGGI  SG  R  + Y  +
Sbjct: 426 RIFRVGEALEYGMVGVN---TGLISNEVAPFGGIKQSGLGREGSKYGLE 471


Lambda     K      H
   0.319    0.135    0.409 

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: 667
Number of extensions: 37
Number of successful extensions: 7
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: 489
Length of database: 483
Length adjustment: 34
Effective length of query: 455
Effective length of database: 449
Effective search space:   204295
Effective search space used:   204295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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