GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuB in Novosphingobium barchaimii LL02

Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate WP_059151132.1 V474_RS08780 mannitol dehydrogenase family protein

Query= ecocyc::MANNONOXIDOREDUCT-MONOMER
         (486 letters)



>NCBI__GCF_001046635.1:WP_059151132.1
          Length = 476

 Score =  307 bits (786), Expect = 6e-88
 Identities = 197/468 (42%), Positives = 257/468 (54%), Gaps = 21/468 (4%)

Query: 11  VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIE 70
           VARP +D + L   +VH G GAFHRAHQA     LL   D  WGI  V+L   N R + +
Sbjct: 16  VARPQYDRAALRGGVVHFGPGAFHRAHQAAAFDTLL-GHDPRWGITGVSL---NSRGVAD 71

Query: 71  NLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEK 130
            L  Q  LYT+A    E TE ++IGS+   L  +  G   IL A+A   T IVS TVTEK
Sbjct: 72  ALNPQGGLYTLALL-EEQTEFRVIGSIGRVLTRDEPGA--ILGALAHGDTRIVSSTVTEK 128

Query: 131 GYCADAASGQLDLNNPLIKHDLENPTA----PKSAIGYIVEALRLRREKGLKAFTVMSCD 186
           GYC  +A G LD  +P I+ DL+   +    P S IG++V  LR RR  GL   TV+SCD
Sbjct: 129 GYCL-SADGTLDFAHPAIRADLDAAKSADWVPGSFIGWLVHGLRARRLAGLLGVTVLSCD 187

Query: 187 NVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGV 246
           N+ +NG   + A + LA+A DP+ A WI   V FP  MVD I PA        +A   G+
Sbjct: 188 NLTDNGRKLEAATIALAEAIDPETARWIAGEVCFPNAMVDSITPATDDALRARVAAATGL 247

Query: 247 YDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLG 306
            D   I  E F QWVIED F   RP  +  G  F  +V PFE  KLR+LNG+HS LAY+G
Sbjct: 248 EDAWPIQRERFTQWVIEDRFAGERPALECAGVTFAGEVRPFETAKLRLLNGAHSSLAYIG 307

Query: 307 YLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHR 366
              G+ET+A+ + +P     A  LM ++ AP++S P G DL  Y   ++ RF+NP++RH 
Sbjct: 308 LGLGFETVAEAMADPGLAAFAERLMREDIAPSVSAPPGLDLPVYIADVLARFANPAIRHL 367

Query: 367 TWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPM 426
             QIA DGSQKLP RLLD  R  L  G     LAL +A W+R+       G +I   DP+
Sbjct: 368 LSQIAWDGSQKLPYRLLDTTRDALVAGRPVDRLALPIAAWLRFLDRAARSGGSI--TDPL 425

Query: 427 LAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQL 474
                      + A   + ++G+  IF  DL ++A F+ AV A    L
Sbjct: 426 SGPL------LERAGDWRRVVGMREIFG-DLGEDARFLRAVEAGLAAL 466


Lambda     K      H
   0.320    0.135    0.408 

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: 623
Number of extensions: 30
Number of successful extensions: 4
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: 486
Length of database: 476
Length adjustment: 34
Effective length of query: 452
Effective length of database: 442
Effective search space:   199784
Effective search space used:   199784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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