GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Hafnia paralvei ATCC 29927

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_008815709.1 M988_RS20750 glutamine--fructose-6-phosphate transaminase (isomerizing)

Query= reanno::pseudo3_N2E3:AO353_04455
         (336 letters)



>NCBI__GCF_001655005.1:WP_008815709.1
          Length = 610

 Score =  127 bits (320), Expect = 6e-34
 Identities = 98/309 (31%), Positives = 156/309 (50%), Gaps = 21/309 (6%)

Query: 41  VARGSSDHAASYFAYLTMQHVGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSGQSPDLV 100
           +A G+S H+     Y      G+P      S    +++ ++     +   SQSG++ D +
Sbjct: 300 IACGTSYHSGMVARYWFESLAGVPCDVEIASEFRYRKSAVR-KNSLIITLSQSGETADTL 358

Query: 101 NSLRLLRKRGAL-SISMVNAENSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLI 159
            +LRL ++ G L S+++ N  +S L    + +L   AGTE  VA+TK+F   L+    L+
Sbjct: 359 AALRLSKEIGYLGSLAICNVASSSLVRESDLALMTKAGTEIGVASTKAFTTQLTVLLMLV 418

Query: 160 AYW--------KQDPELLQAGLALPEGLRDAATQDWS---LAVDVLRDCQRLMVIGRGAG 208
           A          K + +++ A  ALP  +    + D     LA D + D Q  + +GRG  
Sbjct: 419 ARIGRLHTMPEKVEQDIVHALQALPARIEQMLSMDQGIEDLAEDFM-DKQHALFLGRGDQ 477

Query: 209 FAIAQEAALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPLLVFAPRGAEQAGLLSLAAE 268
           + IA E ALKLKE S I AEA+++ E+KHGP+ALID + P++V AP       L S   E
Sbjct: 478 YPIAMEGALKLKEISYIHAEAYAAGELKHGPLALIDADMPVVVIAPNNELLEKLKSNIEE 537

Query: 269 MRQRGARVLLAAPDDVSERD------LTLSRAEHPALDPILAIQSFYVMAAGLAVARGMD 322
           +R RG  + + A  D    D      ++L   E   + PI       +++  +A+ +G D
Sbjct: 538 VRARGGLLYVFADKDAGFTDSEGMRIISLPHVEE-VIAPIFYTVPLQLLSYHVALIKGTD 596

Query: 323 PDQPRHLSK 331
            DQPR+L+K
Sbjct: 597 VDQPRNLAK 605


Lambda     K      H
   0.318    0.130    0.362 

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: 383
Number of extensions: 20
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: 336
Length of database: 610
Length adjustment: 33
Effective length of query: 303
Effective length of database: 577
Effective search space:   174831
Effective search space used:   174831
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 (21.8 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