GapMind for catabolism of small carbon sources

 

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

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate H281DRAFT_02680 H281DRAFT_02680 succinate semialdehyde dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_02680
          Length = 492

 Score =  659 bits (1700), Expect = 0.0
 Identities = 326/480 (67%), Positives = 380/480 (79%), Gaps = 2/480 (0%)

Query: 2   QLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKAL 61
           +L D  L R  A+IDG W  AD+ +T  V++PATGE +  VP M  AETRRAIEA + A 
Sbjct: 11  RLADPSLLRTLAYIDGQWCGADDARTFAVDDPATGEKIADVPLMTGAETRRAIEAGEHAQ 70

Query: 62  PAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAE 121
             WR LTA +R+T L+RW+ L+I N DDL  +M+ EQGKPLAEAKGEI YAASFIEWFAE
Sbjct: 71  RGWRKLTAAQRSTILKRWHALMIANTDDLAIIMSAEQGKPLAEAKGEIGYAASFIEWFAE 130

Query: 122 EAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKP 181
           +AKR+ GDV+     DKR++V K+PIGV AAITPWNFPAAMITRK  PALAAGC M++KP
Sbjct: 131 QAKRVDGDVLASPAADKRMLVTKEPIGVCAAITPWNFPAAMITRKVAPALAAGCAMILKP 190

Query: 182 ASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQL 241
           A  TP SALAL ELAHRAG+P GV SVV G    IG E+TSNPIVRKLSFTGST +GR L
Sbjct: 191 AEATPLSALALAELAHRAGVPAGVFSVVVGDPRSIGAEMTSNPIVRKLSFTGSTPVGRML 250

Query: 242 MAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSV 301
           M++CA  +KK+SLELGGNAPFIVFDDADLD AVEGA+ SKYRN GQTCVC NR+Y+QD V
Sbjct: 251 MSQCAPTVKKLSLELGGNAPFIVFDDADLDAAVEGALASKYRNAGQTCVCTNRVYVQDGV 310

Query: 302 YDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKSM 361
           YDAFAEK  AAV ++K+GNG E G T GPLI+E AV KV+ HIADA+  GA +L GGK  
Sbjct: 311 YDAFAEKFAAAVGRIKVGNGFESGVTQGPLINEAAVEKVEAHIADAVAHGARVLTGGKRH 370

Query: 362 EGN--FFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419
                FFEPT++ +V      A EETFGP+APLFRF +E E IA +N TEFGLA+YFY+R
Sbjct: 371 AAGKLFFEPTVVGDVTARMRFATEETFGPVAPLFRFTNEREAIAAANATEFGLAAYFYSR 430

Query: 420 DLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479
           D+GR++RVAEALEYGMVG+NTGLISNEVAPFGG+K SGLGREGSKYGIEDYLEIKYLC+G
Sbjct: 431 DIGRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSKYGIEDYLEIKYLCMG 490


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: 702
Number of extensions: 13
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: 492
Length adjustment: 34
Effective length of query: 446
Effective length of database: 458
Effective search space:   204268
Effective search space used:   204268
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