GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Escherichia coli BW25113

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>FitnessBrowser__Keio:16751
          Length = 482

 Score =  798 bits (2062), Expect = 0.0
 Identities = 397/482 (82%), Positives = 439/482 (91%), Gaps = 2/482 (0%)

Query: 1   MQLKDTQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60
           M+L D+ LFRQQA I+G W+DA+NG+ I V NPA G+ LG+VPKMGA ETR AI+AA++A
Sbjct: 1   MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60

Query: 61  LPAWRALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFA 120
           LPAWRALTAKERAT LR W+ L++E+QDDLARLMTLEQGKPLAEAKGEI YAASFIEWFA
Sbjct: 61  LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE KRIYGD IPGHQ DKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK
Sbjct: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180

Query: 181 PASQTPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQ 240
           PASQTPFSA ALAELA RAG+PAGVF+VV+GSAG +G+ELTSNP+VRKLSFTGSTEIGRQ
Sbjct: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQ 240

Query: 241 LMSECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDG 300
           LM +CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGA+ SK+RN GQTCVCANRLY+QDG
Sbjct: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDG 300

Query: 301 VYDAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKP 360
           VYD FAEKL+ AV+KL IG+GL+ G T GPLIDEKAVAKV+EHIADAL KGA V+ GGK 
Sbjct: 301 VYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKA 360

Query: 361 ME--GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYA 418
            E  GNFF+PTIL +VP NA V+KEETFGPLAPLFRFKDEADVIA +NDTEFGLA+YFYA
Sbjct: 361 HERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYA 420

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           RDL RVFRV EALEYG+VG+NTG+ISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY+C+
Sbjct: 421 RDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCI 480

Query: 479 GI 480
           G+
Sbjct: 481 GL 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: 787
Number of extensions: 24
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 (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