GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF 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)



>lcl|FitnessBrowser__ANA3:7025959 Shewana3_3107
           methylmalonate-semialdehyde dehydrogenase [acylating]
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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