GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Herbaspirillum seropedicae SmR1

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate HSERO_RS22125 HSERO_RS22125 glucosamine--fructose-6-phosphate aminotransferase

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



>FitnessBrowser__HerbieS:HSERO_RS22125
          Length = 605

 Score =  133 bits (334), Expect = 1e-35
 Identities = 104/312 (33%), Positives = 157/312 (50%), Gaps = 22/312 (7%)

Query: 51  VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110
           ++  A G+S +A   AKY +E++  +P      S     D+   P   L + ISQSG++ 
Sbjct: 291 ILILACGTSYYAGLTAKYWLESIAKIPVNVEIASEYRYRDSVPNP-KSLVVTISQSGETA 349

Query: 111 DLLATVEHQRKAGA-FVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIA 169
           D LA ++H R  G    + + N   S +    ++    +AG E  VA+TK++   LAA+ 
Sbjct: 350 DTLAALKHARSLGMQHTLTICNVATSAMVRECELAYITRAGVEVGVASTKAFTTQLAALF 409

Query: 170 ALVAAWAQDEALET---------AVADLPAQLERAFALDWSAAVTALTGA---SGLFVLG 217
            L  A AQ   L T         A+  LPA L+   AL+ S    A + A   + LF LG
Sbjct: 410 LLTLALAQTRGLLTEEQEAEHLKAMRHLPAALQSVLALEPSIVAWAESFARRENALF-LG 468

Query: 218 RGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRE 277
           RG  Y IA E ALK KE   +HAE+++A E++HGP+A+V +   V+  A +D   E ++ 
Sbjct: 469 RGLHYPIALEGALKLKEITYIHAEAYAAGELKHGPLALVTDQMPVVTIAPNDALVEKLKS 528

Query: 278 TVAEFRSRGAEV-LLAD---PAARQAGLPAIAA---HPAIEPILIVQSFYKMANALALAR 330
            + E R+RG ++ + AD     +   GL  I     +  + PIL V     ++   ALAR
Sbjct: 529 NMQEVRARGGQLYVFADGDSHISSAEGLHVIRMPEHYGVLSPILHVVPLQLLSYHTALAR 588

Query: 331 GCDPDSPPHLNK 342
           G D D P +L K
Sbjct: 589 GTDVDKPRNLAK 600


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: 384
Number of extensions: 23
Number of successful extensions: 5
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: 605
Length adjustment: 33
Effective length of query: 314
Effective length of database: 572
Effective search space:   179608
Effective search space used:   179608
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