GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Pseudomonas stutzeri RCH2

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase

Query= curated2:Q12QD2
         (498 letters)



>lcl|FitnessBrowser__psRCH2:GFF2584 Psest_2634 glycine betaine
           aldehyde dehydrogenase
          Length = 490

 Score =  211 bits (536), Expect = 6e-59
 Identities = 158/458 (34%), Positives = 229/458 (50%), Gaps = 13/458 (2%)

Query: 12  QTQFIAGQWL-AGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLT 70
           Q  +I G ++ A    +F S+NPANGEV+ Q   A A  ++ A+ SA      W+A++  
Sbjct: 7   QQLYIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTGI 66

Query: 71  ERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKAN-AERTGT 129
           ER  I+    + L+E  +  A    L+TGK L E+R+ V  +TG   +   A  A     
Sbjct: 67  ERARIMRRAVDLLRERNDELALLETLDTGKPLSETRS-VDIVTGADVLEYYAGLAPAIEG 125

Query: 130 VENPMPGAK-AFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188
            + P+  +   + R +P GVVA  G +N+P  +      PAL AGN ++FKPSE+T   A
Sbjct: 126 EQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSA 185

Query: 189 ELTMQLWQQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQP 247
               +++ +AGLP+GV N+L G  A  G  +  H  I  + FTG   TG  +    A   
Sbjct: 186 LKLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSS 245

Query: 248 GKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILA 307
            K + +E+GG +PLII E A++D A    + + F SSGQ CT   R+F+P      A  A
Sbjct: 246 LKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKA-AFEA 304

Query: 308 KLLTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGL- 366
           KLL    +I LGDP  E +  FG ++S      ++   A  +AAG   L    +VT G  
Sbjct: 305 KLLERVQRIRLGDPQQE-ETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEY 363

Query: 367 ---GFVTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADS 422
               FV P I  D +D   +  EE FGP+L +  Y D D  I  AN+T +GL+AG++   
Sbjct: 364 AKGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTAD 423

Query: 423 ETDYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASG 460
                    R+ AGI  W      + +  P GG   SG
Sbjct: 424 LARAHRIIHRLEAGIC-WINTWGESPAQMPVGGYKQSG 460


Lambda     K      H
   0.317    0.133    0.390 

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: 566
Number of extensions: 23
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 498
Length of database: 490
Length adjustment: 34
Effective length of query: 464
Effective length of database: 456
Effective search space:   211584
Effective search space used:   211584
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 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 paper from 2022 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