GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate Echvi_1524 Echvi_1524 glucosamine--fructose-6-phosphate aminotransferase (isomerizing)

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



>FitnessBrowser__Cola:Echvi_1524
          Length = 613

 Score =  135 bits (340), Expect = 3e-36
 Identities = 95/310 (30%), Positives = 152/310 (49%), Gaps = 19/310 (6%)

Query: 51  VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110
           ++  A G+S HA   A+YL E    VP      S    Y  PV       +AISQSG++ 
Sbjct: 300 IIITACGTSWHAGLVAEYLFEEFARVPVEVEYASEFR-YRNPVINSRDFVIAISQSGETA 358

Query: 111 DLLATVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIA- 169
           D LA +E  ++ GA +  + N   S +A          AGPE  VA+TK++   ++ ++ 
Sbjct: 359 DTLAAIELAKQKGATIFGVCNVVGSSIARATHAGSYTHAGPEIGVASTKAFTAQISVLSM 418

Query: 170 -ALVAAWAQDEALETAVADL-------PAQLERAFALDWSAAVTALT--GASGLFVLGRG 219
            AL+  + +    E+   +L       PA++E+A  L+      A     A     LGRG
Sbjct: 419 MALMLGYQRGTLPESKYMELLSELEAIPAKVEKALKLNEQIERIAAQYKDARNFLYLGRG 478

Query: 220 YGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETV 279
           Y + +A E ALK KE   +HAE + AAE++HGP+A++ E   V+  A+ D + E V   +
Sbjct: 479 YNFPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDEEMPVVFIATQDSSYEKVVSNI 538

Query: 280 AEFRSRGAEVLL----ADPAARQAGLPAI---AAHPAIEPILIVQSFYKMANALALARGC 332
            E ++R  +++      D   R+     I    AH A  P++ V    +++  +A+ RGC
Sbjct: 539 QEVKARKGKIIAVVTEGDQTVRKMADHVIEIPRAHEAFVPLISVLPLQQLSYHIAVMRGC 598

Query: 333 DPDSPPHLNK 342
           + D P +L K
Sbjct: 599 NVDQPRNLAK 608


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: 372
Number of extensions: 19
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: 347
Length of database: 613
Length adjustment: 33
Effective length of query: 314
Effective length of database: 580
Effective search space:   182120
Effective search space used:   182120
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: 51 (24.3 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