GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Novosphingobium barchaimii LL02

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_059151198.1 V474_RS09170 SIS domain-containing protein

Query= reanno::Korea:Ga0059261_1644
         (347 letters)



>NCBI__GCF_001046635.1:WP_059151198.1
          Length = 358

 Score =  302 bits (773), Expect = 1e-86
 Identities = 181/342 (52%), Positives = 217/342 (63%), Gaps = 6/342 (1%)

Query: 12  TLMEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCARGSSDHAATYAKYLIE 71
           T M REA EA A  ++ L  N D +     +LR   P    T ARGSSD AA +AK+L+E
Sbjct: 17  TQMAREAREAPALCAQQLRLNADLVRDAGRQLRDLAPPFAATLARGSSDQAAAFAKFLLE 76

Query: 72  TLTGVPTASAALSVASLYDAPVAPGNGLCL-AISQSGKSPDLLATVEHQRKAGAFVVAMV 130
           T   VPT S A SV SLY A  A    + L AISQSG+SPDLLA  +  R+ GA V+A+V
Sbjct: 77  THARVPTLSHAPSVGSLYHATSANFRNVPLIAISQSGRSPDLLAAAKDAREQGAIVIAVV 136

Query: 131 NAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEALETAVADLPA 190
           N   SPLA LA IVIP+ AGPE SVAATKS++C L A+  L A W+QDEAL  A+     
Sbjct: 137 NDAASPLAQLAQIVIPVHAGPETSVAATKSFVCMLVALTHLAAEWSQDEALLAALESTGE 196

Query: 191 QLERAFALDWSAAVTALTGASGLFVLGRGYGYGIAQEAALKFKETCALHAESFSAAEVRH 250
            LE A   DW+ AVT L  AS + VLGRG    IA EAALK KET +LHAE+FS AEV H
Sbjct: 197 VLETAAIADWTDAVTLLQDASEMLVLGRGPTLPIAGEAALKLKETSSLHAEAFSIAEVAH 256

Query: 251 GPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLA----DPAARQAGLPA-IA 305
           GPM +VGE   VLA A  D A   +R+ +A+F +RGA V+ A    D A     LP+   
Sbjct: 257 GPMTLVGEGSAVLALAPLDVARTGLRDRLADFAARGAHVIAAGAPEDVAPAGLVLPSRTD 316

Query: 306 AHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNKVTETL 347
            HP +  I  +QSFY +ANAL+LARG +PDSPPHLNKVT TL
Sbjct: 317 VHPVLGAIAQIQSFYGLANALSLARGRNPDSPPHLNKVTRTL 358


Lambda     K      H
   0.317    0.128    0.360 

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: 367
Number of extensions: 14
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: 347
Length of database: 358
Length adjustment: 29
Effective length of query: 318
Effective length of database: 329
Effective search space:   104622
Effective search space used:   104622
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: 49 (23.5 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