GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Pseudomonas stutzeri RCH2

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate GFF4164 Psest_4237 succinate-semialdehyde dehydrogenase

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



>lcl|FitnessBrowser__psRCH2:GFF4164 Psest_4237
           succinate-semialdehyde dehydrogenase
          Length = 482

 Score =  819 bits (2115), Expect = 0.0
 Identities = 404/482 (83%), Positives = 446/482 (92%), Gaps = 2/482 (0%)

Query: 1   MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60
           MQLKD  LFRQQA+IDGAW+DAD+GQTI VNNPATGE LGTVPKMGAAETRRAI+AA++A
Sbjct: 1   MQLKDTALFRQQAYIDGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERA 60

Query: 61  LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120
           LPAWR LTAKER+ KLRRW+ELL+ENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA
Sbjct: 61  LPAWRDLTAKERSQKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180
           EEAKRIYGD IPGHQ DKR+IVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK
Sbjct: 121 EEAKRIYGDTIPGHQKDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180

Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240
           PASQTPFSALA+VELA RAGIPKGVLSVVTGSAGDIG ELT+NP VRK+SFTGSTE+G +
Sbjct: 181 PASQTPFSALAMVELAERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAK 240

Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300
           LM +CA  IKKVSLELGGNAPFIVFDDADLD+AV+GA+ SKYRN GQTCVC NR+Y+QD 
Sbjct: 241 LMEQCAPGIKKVSLELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDG 300

Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359
           VYD FAEK +AAVAKL++GNGLEEGT  GPLID++A AKV+EHI DA+ +GA L+AGG+ 
Sbjct: 301 VYDTFAEKFQAAVAKLRVGNGLEEGTDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQA 360

Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            ++ G++FEPT+LVNVP  A VAKEETFGPLAPLFRFKDEA+ IA +NDTEFGLASYFYA
Sbjct: 361 HALGGSYFEPTVLVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYA 420

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           RDLGRVFRVAEALEYGMVG+NTGLIS EVAPFGG+K+SGLGREGSKYGIEDYLEIKYLC+
Sbjct: 421 RDLGRVFRVAEALEYGMVGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYLCM 480

Query: 479 GI 480
           GI
Sbjct: 481 GI 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: 805
Number of extensions: 18
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: 482
Length adjustment: 34
Effective length of query: 446
Effective length of database: 448
Effective search space:   199808
Effective search space used:   199808
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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