GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF3462
          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:

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