GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Shewanella sp. ANA-3

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= reanno::MR1:200453
         (482 letters)



>FitnessBrowser__ANA3:7025944
          Length = 482

 Score =  900 bits (2327), Expect = 0.0
 Identities = 452/482 (93%), Positives = 461/482 (95%)

Query: 1   MLLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAA 60
           MLL DPSLLRQQCYINGQWCDA SKETVAI NPATGAVIA VPVMGQAETQAAIAAAEAA
Sbjct: 1   MLLKDPSLLRQQCYINGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAA 60

Query: 61  LPAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFA 120
           LPAWRALTAKERG KLRRWFELLNENSDDLAL+MTSEQGKPL EAKGEVTYAASFIEWFA
Sbjct: 61  LPAWRALTAKERGVKLRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFA 120

Query: 121 EEAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180
           EEAKR+YGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK
Sbjct: 121 EEAKRVYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180

Query: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240
           PAPQTPFTALALAVLAERAGIPAGVFSVITGDAI IGNEMC+NP+VRKLSFTGST VGIK
Sbjct: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIK 240

Query: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300
           LM QCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG
Sbjct: 241 LMEQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300

Query: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360
           VYDEFA KLS+AV KLKVGEGI  GVTTGPLIN AAVEKVQSHLEDA+ KGATV+AGGK 
Sbjct: 301 VYDEFARKLSIAVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGKP 360

Query: 361 HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG 420
           H LGGNFFEPTVLTN D SMRVAREETFGPLAPLFKF DVDDVIKQANDTEFGLAAYFYG
Sbjct: 361 HSLGGNFFEPTVLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYG 420

Query: 421 RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480
           RDISLVWKV E+LEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSK+GIEEYLEIKYICM
Sbjct: 421 RDISLVWKVTEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKFGIEEYLEIKYICM 480

Query: 481 SV 482
           SV
Sbjct: 481 SV 482


Lambda     K      H
   0.318    0.133    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: 844
Number of extensions: 20
Number of successful extensions: 1
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: 482
Length of database: 482
Length adjustment: 34
Effective length of query: 448
Effective length of database: 448
Effective search space:   200704
Effective search space used:   200704
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