GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Marinobacter adhaerens HP15

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF3462 HP15_3404 succinic semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__Marino:GFF3462 HP15_3404 succinic semialdehyde
           dehydrogenase
          Length = 483

 Score =  404 bits (1038), Expect = e-117
 Identities = 210/463 (45%), Positives = 289/463 (62%), Gaps = 2/463 (0%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           Y+ G W D ++G T  V NPATG++I  V  M   E   A+ +   AL      + + R 
Sbjct: 13  YIGGRWTDNEHGNTFDVYNPATGKVIAQVASMSEDEVNAAVASGKSALRLTSPYSIETRR 72

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133
             L    D +  N++++ R++ +E GKPL EA+GE+ YAA F ++  +  + +   TIP 
Sbjct: 73  KWLEDIRDALKANKEEVGRILCMEHGKPLQEAQGEVDYAAGFFDYCSKHIQALDAHTIPE 132

Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193
              D    V  +PIGVT  ITPWNFP  MI +K   ALAAGC  V+KPAS+TP + +AL 
Sbjct: 133 KPKDCTWTVHYRPIGVTGLITPWNFPIGMIAKKLSAALAAGCPSVIKPASETPLTMIALF 192

Query: 194 ELAER-AGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252
            L ++   IP G+ ++V G A  +G  L  +P V  L+FTGSTE+GR+L+ + A  +KK+
Sbjct: 193 SLMDKHTDIPDGMVNLVMGKASVIGKVLCESPDVPMLSFTGSTEVGRKLIVDTADQVKKL 252

Query: 253 SLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312
           +LELGGNAPFIVFDDADLDAA +  + +K+R  GQTCVCANR++V + V DAF +KL   
Sbjct: 253 ALELGGNAPFIVFDDADLDAAADNLIANKFRGGGQTCVCANRIFVHEKVADAFGEKLAER 312

Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGG-TFFEPT 371
           V K+ +G+G+   V  GPLI+     KV+ H+ DA+ KGA +V+G KP  LG   FF PT
Sbjct: 313 VNKMTVGDGINGDVDLGPLINQAGYDKVKRHVQDALEKGATLVAGKKPEDLGNDLFFPPT 372

Query: 372 ILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAE 431
           ++  V ++    ++ETFGPL P+  F+ E EVI   NDTEFGLASY +  D  R  RVA 
Sbjct: 373 VVHGVNRDMCCYQEETFGPLVPMALFRTEEEVIEAGNDTEFGLASYVFTNDAERAQRVAA 432

Query: 432 QLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 474
            L +G  G NTG      APFGG+KASG+GREG   G+ +++E
Sbjct: 433 GLRFGHCGWNTGTGPTPEAPFGGMKASGIGREGGLEGLFEFVE 475


Lambda     K      H
   0.317    0.135    0.391 

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: 642
Number of extensions: 26
Number of successful extensions: 3
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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 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