GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS05395
          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.

Links

Downloads

Related tools

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