GapMind for catabolism of small carbon sources

 

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

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1109
         (481 letters)



>FitnessBrowser__ANA3:7025959
          Length = 496

 Score =  279 bits (714), Expect = 1e-79
 Identities = 172/467 (36%), Positives = 245/467 (52%), Gaps = 4/467 (0%)

Query: 9   NYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARH 68
           +Y+NGE  + +  S  I      +  G  + A   +V AAI  A++AF  WS      R 
Sbjct: 6   HYVNGEHTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVTPLNRA 65

Query: 69  DSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPS 128
             L K    +    +EL  L+  E GK L +A GE+ R   + +F  G    L G++   
Sbjct: 66  RVLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKGEHTEQ 125

Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALA 188
           V  GV+     +ALGVV  I P+NFP+ +P W    A+A GN  ++KP++  P     +A
Sbjct: 126 VGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSAVMRIA 185

Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248
           E++++AG PAGVFN+V G    V D L+    +  +SF GS  +   I  +      +VQ
Sbjct: 186 ELLTQAGLPAGVFNVVNGDKEAV-DTLLSHEDIQAVSFVGSTPIAEYIYSTASKHGKRVQ 244

Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERM 308
              G KN  +++ DADL QAV   + +A+ S G+RC A S  +    + DK V+ +  ++
Sbjct: 245 ALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQI 304

Query: 309 KSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGG--LVACDTEGYFLA 366
           + +KVG+ L    ++GP++S+  L +  +++D G  EGA LV  G    VA   +GYFL 
Sbjct: 305 QQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLG 364

Query: 367 PTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHF 426
             LF + T  MRI REEIFGPV +IVRV DY +ALA+ N  EFG    I T S + A HF
Sbjct: 365 ACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGEAARHF 424

Query: 427 KRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYT 472
             H Q GMV VN+P         FGG K S +G     G     FYT
Sbjct: 425 CHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYT 471


Lambda     K      H
   0.318    0.134    0.391 

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: 525
Number of extensions: 20
Number of successful extensions: 3
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: 481
Length of database: 496
Length adjustment: 34
Effective length of query: 447
Effective length of database: 462
Effective search space:   206514
Effective search space used:   206514
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