GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Dinoroseobacter shibae DFL-12

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= curated2:Q1QTQ7
         (489 letters)



>lcl|FitnessBrowser__Dino:3609503 Dshi_2887 succinic semialdehyde
           dehydrogenase (RefSeq)
          Length = 492

 Score =  190 bits (483), Expect = 8e-53
 Identities = 151/465 (32%), Positives = 226/465 (48%), Gaps = 22/465 (4%)

Query: 11  GAWVDGDA-ARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFAERQAVV 69
           GAW D D+ A F  T+P  G+ +         +   A+AAA  A   WA R+  +R  V+
Sbjct: 26  GAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVL 85

Query: 70  ERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERT--GER-ARD 126
            R+ + +  + + LA  +  E GKPL EAR EV  M G   +   A   +   GE     
Sbjct: 86  RRWFDLIVGNADDLARILTAEMGKPLAEARGEV--MYGASFVEWFAEEAKRLYGETIPGH 143

Query: 127 IGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTADLTLQ 186
           + DAR  +  +P GV+    P+NFP  +      PAL AG A + KP+E TP++A     
Sbjct: 144 LPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALAV 203

Query: 187 CWLEAGLPAGVINLV--QGAAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVDKIL 244
               AG+PAG+  ++    ++ +G+    +  +  L FTGS +VG +L  Q   QV K  
Sbjct: 204 LAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKK-C 262

Query: 245 ALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDALTS 304
           ++ELGGN P +V D  D + AV   +   F + GQ C CA R+ V  G V D   + L +
Sbjct: 263 SMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDG-VYDAFAEKLAA 321

Query: 305 AIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQAGTSLLSP 364
           A+ EL+V    +E       L ++ A + +    DDL A+GG  ++       G +  +P
Sbjct: 322 AVEELKVGDGAAEGVTI-GPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTP 380

Query: 365 GLIDVTG----CDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGERADWDD 420
            +  VTG      V  EE FGP+  + R+ + DE IA+ANDT +GL+      +      
Sbjct: 381 TV--VTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITR 438

Query: 421 FLLRIRAGIVNWNRQTTG--ASSDAPFGGIGDSGNHRPSAYYAAD 463
               +  GIV  N   TG  ++  APFGG+  SG  R  + +  D
Sbjct: 439 VSEALEYGIVGIN---TGIISTEGAPFGGVKQSGLGREGSRHGID 480


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: 646
Number of extensions: 25
Number of successful extensions: 6
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: 492
Length adjustment: 34
Effective length of query: 455
Effective length of database: 458
Effective search space:   208390
Effective search space used:   208390
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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