GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Williamsia sterculiae CPCC 203464

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_076476938.1 BW971_RS04495 glutamine--fructose-6-phosphate transaminase (isomerizing)

Query= reanno::Caulo:CCNA_00453
         (363 letters)



>NCBI__GCF_900156495.1:WP_076476938.1
          Length = 620

 Score =  141 bits (356), Expect = 4e-38
 Identities = 117/330 (35%), Positives = 169/330 (51%), Gaps = 36/330 (10%)

Query: 56  QRLRANPPRVVVTCARGSSDHAATFARYLIE--TKAGVLTSSAGPSVSSVYDASPNLE-G 112
           Q LR      VV C  G++ HA   A+Y IE  T+  V    A    S      P L+  
Sbjct: 295 QDLRDVDKVFVVAC--GTAYHAGLIAKYAIEHWTRLPVEVELA----SEFRYRDPVLDRS 348

Query: 113 ALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAA 172
            L +AISQSG++ D L AV+ AK   A  +A+ N   + +   +D V+  HAGPE+ VA+
Sbjct: 349 TLVVAISQSGETADTLEAVRHAKEQKARVLAICNTNGAQIPRESDAVLYTHAGPEIGVAS 408

Query: 173 TKSYIAALVAVTQLIAAWTEDAELTA----------ALQDLPTALAAAW-TLDWSLAVER 221
           TK ++A +VA T L+      A  T           AL+ +  A+A    T++   A+ R
Sbjct: 409 TKCFLAQIVA-TYLVGLALAQARGTKYSDEVAREYLALEQMTDAVAQVLETVEPVRALAR 467

Query: 222 -LKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVF 280
            L +   +  LGR VG+ VALE ALK KE   +HAE F+A E+ HGP+AL++DG P +V 
Sbjct: 468 DLSSTDTVLFLGRHVGYPVALEGALKLKELAYIHAEGFAAGELKHGPIALIEDGVPVIVV 527

Query: 281 AQNDESRASV-DEMAAGLR---ARGASVLIAGGGGDAPDALPTLASH--------PVLEP 328
             +   RA +  +M + +R   ARGA+ ++    GD   A   LA H         +L+P
Sbjct: 528 MPSPVGRAVLHSKMVSNIREIQARGATTIVIAEDGDI--AAAALADHLIVIPRVPTLLQP 585

Query: 329 ILMIQSFYRMANALSVARGYDPDSPPHLNK 358
           ++        A A++ ARGYD D P +L K
Sbjct: 586 LVSTVPLQAFAAAVAQARGYDVDKPRNLAK 615


Lambda     K      H
   0.315    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: 416
Number of extensions: 18
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: 363
Length of database: 620
Length adjustment: 33
Effective length of query: 330
Effective length of database: 587
Effective search space:   193710
Effective search space used:   193710
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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