GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxD in Paraburkholderia bryophila 376MFSha3.1

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate H281DRAFT_00370 H281DRAFT_00370 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (EC 1.2.1.77)

Query= BRENDA::Q13WK4
         (531 letters)



>FitnessBrowser__Burk376:H281DRAFT_00370
          Length = 531

 Score =  905 bits (2340), Expect = 0.0
 Identities = 457/531 (86%), Positives = 491/531 (92%)

Query: 1   MTELLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRAL 60
           M ELLKNHVAG+W+AGTG G TLTDPVTG ALVRVSSEGLDL+ AF FAR++ G +LRAL
Sbjct: 1   MIELLKNHVAGEWVAGTGDGHTLTDPVTGEALVRVSSEGLDLSHAFRFARDEAGPSLRAL 60

Query: 61  TYAQRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120
           TYA+RAARLAD+VKLLQ+KR DYYAIA ANSGTTRNDSAVDIDGGIFTLSYYA+LGASLG
Sbjct: 61  TYAERAARLADVVKLLQSKRDDYYAIALANSGTTRNDSAVDIDGGIFTLSYYARLGASLG 120

Query: 121 EVHALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180
            VHALRDG+A +LSKD+SFS QHVL+PTRGVALFINAFNFPSWGLWEKAAPALLSG+PVI
Sbjct: 121 NVHALRDGNASALSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGLPVI 180

Query: 181 VKPATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAAT 240
           VKPATATAWLTQRM+ADVVDAGILP GALS+ICG SAGLLDQ+++FDVVSFTGSA+TAA+
Sbjct: 181 VKPATATAWLTQRMIADVVDAGILPRGALSVICGGSAGLLDQVQAFDVVSFTGSAETAAS 240

Query: 241 LRAHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300
           LRAHPAFV RGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR
Sbjct: 241 LRAHPAFVVRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300

Query: 301 RAFVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVL 360
           RAFVP+ AL+ V++ALK KLAKITVGNPRNDAVRMGSLVSR QYENVLAGIAALR+EAVL
Sbjct: 301 RAFVPDTALDAVVDALKTKLAKITVGNPRNDAVRMGSLVSRAQYENVLAGIAALRQEAVL 360

Query: 361 AYDSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420
           AYD SA PLIDADA +AAC+APHLFVVNDPDNATLLHDVEVFGPVASVAPY V      L
Sbjct: 361 AYDGSAAPLIDADAAVAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYCVANGAGEL 420

Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480
            EAHAV LARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHA+SPSV+ SQTGHGNVM
Sbjct: 421 REAHAVDLARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAVSPSVEQSQTGHGNVM 480

Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQATHWPAA 531
           PMSLHGGPGRAGGGEELGGLRAL FYHRRSAIQA++AAI  + Q TH P A
Sbjct: 481 PMSLHGGPGRAGGGEELGGLRALGFYHRRSAIQASAAAIDAVAQLTHLPTA 531


Lambda     K      H
   0.318    0.132    0.379 

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: 904
Number of extensions: 16
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: 531
Length of database: 531
Length adjustment: 35
Effective length of query: 496
Effective length of database: 496
Effective search space:   246016
Effective search space used:   246016
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