GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Herbaspirillum seropedicae SmR1

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate HSERO_RS05395 HSERO_RS05395 succinate-semialdehyde dehdyrogenase

Query= metacyc::MONOMER-15736
         (480 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05395 HSERO_RS05395
           succinate-semialdehyde dehdyrogenase
          Length = 484

 Score =  695 bits (1794), Expect = 0.0
 Identities = 342/481 (71%), Positives = 397/481 (82%), Gaps = 2/481 (0%)

Query: 1   MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60
           +QLKD  L RQQAF++G W DAD G+ + V+NPA GE+LG VP MGAAETRRAIEAA+ A
Sbjct: 2   LQLKDPALLRQQAFVNGQWCDADQGERLAVHNPANGELLGHVPLMGAAETRRAIEAANAA 61

Query: 61  LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120
            PAW+  TAKER+  LRRWYEL++ N DDL  +MT EQGKPLAEA+GEI YAASFIEWFA
Sbjct: 62  WPAWKKKTAKERSAILRRWYELMLANTDDLALIMTAEQGKPLAEARGEIGYAASFIEWFA 121

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180
           EE KR YGD IP   P  R++VIK+ IGV AAITPWNFPAAMITRKAGPALAAGC MV+K
Sbjct: 122 EEGKRTYGDTIPSPSPSNRIVVIKEAIGVCAAITPWNFPAAMITRKAGPALAAGCPMVLK 181

Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240
           PA  TPFSALAL  LA RAGIP GV SVVTG+   IGGE+TSNPIVRK+SFTGST +G+ 
Sbjct: 182 PAEATPFSALALAVLAERAGIPAGVFSVVTGTPKGIGGEMTSNPIVRKISFTGSTGVGKL 241

Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300
           LM + A  IKK+SLELGGNAPFIVFDDADLD AVEGAI SKYRN GQTCVCANR+Y+QD 
Sbjct: 242 LMQQSASSIKKLSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRIYVQDG 301

Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359
           VYDAFA KL  AV K K+G G EEG T GPLI+E+AV KV++H+ADA+ KGA +L GGK 
Sbjct: 302 VYDAFAAKLVEAVKKFKVGQGTEEGVTQGPLINEQAVQKVEQHVADAVAKGARVLLGGKR 361

Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            ++  +FFEPT+L +V     VA+EETFGP+APLFRFK + EV+A++NDTEFGLASYFY+
Sbjct: 362 HALGHSFFEPTVLADVTPAMQVAREETFGPMAPLFRFKTDEEVLALANDTEFGLASYFYS 421

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           RD+GR++RVAE LE GMVG+NTGLISNEVAPFGG+K SGLGREGS YGI+DYL +KYLC+
Sbjct: 422 RDIGRIWRVAEGLESGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYLVVKYLCM 481

Query: 479 G 479
           G
Sbjct: 482 G 482


Lambda     K      H
   0.317    0.135    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: 698
Number of extensions: 12
Number of successful extensions: 2
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: 480
Length of database: 484
Length adjustment: 34
Effective length of query: 446
Effective length of database: 450
Effective search space:   200700
Effective search space used:   200700
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