GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609503
          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 (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