GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Marinobacter adhaerens HP15

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= curated2:Q1QTQ7
         (489 letters)



>lcl|FitnessBrowser__Marino:GFF2064 HP15_2020 succinate-semialdehyde
           dehydrogenase I
          Length = 489

 Score =  208 bits (529), Expect = 4e-58
 Identities = 151/468 (32%), Positives = 229/468 (48%), Gaps = 12/468 (2%)

Query: 4   KQQLLIDGAWVDGDAAR-FAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62
           ++Q  I+G W+   + + FA  DP +GE L T      T    A+ AA  A+P W     
Sbjct: 12  REQAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRSTPA 71

Query: 63  AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122
            ER  ++ ++   L  ++E LA  +  E GKPL E+R EVG     +           G+
Sbjct: 72  KERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRAYGD 131

Query: 123 RARDIG-DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTA 181
                G D R V+  +P GV+A   P+NFP  +    + PAL AG  VV KP+E TP++A
Sbjct: 132 VIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTPLSA 191

Query: 182 DLTLQCWLEAGLPAGVINLV----QGAAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFG 237
                   EAG+PAG+IN++      A  VG  L G+  +  + FTGS  VG LL RQ  
Sbjct: 192 LAITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGKLLMRQAS 251

Query: 238 GQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDD 297
             V K+ +LELGGN P +V D  D +AAV  ++ S + + GQ C CA R+ V  G V D 
Sbjct: 252 DTVKKV-SLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQAG-VYDA 309

Query: 298 LIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQA 357
             + L +A++++ V  P  E       L +  A   +    +D  ++G +     R    
Sbjct: 310 FAEKLKAAVSKM-VVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGRAHSL 368

Query: 358 GTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGER 415
           G +   P ++     +  +  EE FGP+  + ++   DEAIA+AND+ +GLSA       
Sbjct: 369 GGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFYSRNI 428

Query: 416 ADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463
                    + +G++  N     ++  APFGG+ +SG  R  ++Y  D
Sbjct: 429 HRVWRVAEELESGMIGVNEGII-STEVAPFGGVKESGLGREGSHYGLD 475


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: 622
Number of extensions: 34
Number of successful extensions: 5
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: 489
Length adjustment: 34
Effective length of query: 455
Effective length of database: 455
Effective search space:   207025
Effective search space used:   207025
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 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