GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Bacteroides clarus YIT 12056

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_009123332.1 BUB52_RS09485 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_900129655.1:WP_009123332.1
          Length = 614

 Score =  112 bits (281), Expect = 2e-29
 Identities = 95/308 (30%), Positives = 152/308 (49%), Gaps = 19/308 (6%)

Query: 41  VARGSSDHAASYFAYLTMQHVGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSGQSPDLV 100
           VA G+S HAA    +L      IPV  +  +     + P+  S   V A SQSG++ D +
Sbjct: 304 VACGTSWHAALIGKHLIESFCRIPV-EVEYASEFRYRDPVIDSSDVVIAISQSGETADTL 362

Query: 101 NSLRLLRKRGALSISMVNAENSPLEAACEFSLPLCAGTESSVAATKSF---IATLSASAR 157
            ++ L + RGA    + NA  S +  A      +  G E  VA+TK+F   +  L+  A 
Sbjct: 363 AAIELAKSRGAFIYGICNAIGSSIPRATNTGSYIHVGPEIGVASTKAFTGQVTVLTMLAL 422

Query: 158 LIAYWKQDPELLQAGLAL-------PEGLRDAATQDWSLAV--DVLRDCQRLMVIGRGAG 208
            +A  K+  +  Q  LA+       P  +++    +  +A    +       + +GRG  
Sbjct: 423 TLAREKRTIDETQY-LAIVRELGQIPGKMKEVLKLNDRIAELSKIFTYVHNFIYLGRGYS 481

Query: 209 FAIAQEAALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPLLVFAPRGAEQAGLLSLAAE 268
           + +A E ALKLKE S I AE + +AE+KHGP+ALID   P++V A +      +LS   E
Sbjct: 482 YPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDAEMPVVVIATQNGLYEKVLSNIQE 541

Query: 269 MRQRGARV--LLAAPDDVSER--DLTLSRAE-HPALDPILAIQSFYVMAAGLAVARGMDP 323
           ++ R  RV  ++   D V  +  D+ +   E    L P++      ++A  +AV +GMD 
Sbjct: 542 IKARKGRVIAIVTKGDTVIGKIADICIELPETMECLGPLITTVPLQLLAYHIAVCKGMDV 601

Query: 324 DQPRHLSK 331
           D+PR+L+K
Sbjct: 602 DRPRNLAK 609


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: 354
Number of extensions: 15
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: 336
Length of database: 614
Length adjustment: 33
Effective length of query: 303
Effective length of database: 581
Effective search space:   176043
Effective search space used:   176043
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