GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Rhodobacter viridis JA737

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_110803821.1 C8J30_RS00730 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_003217355.1:WP_110803821.1
          Length = 603

 Score =  135 bits (340), Expect = 3e-36
 Identities = 110/337 (32%), Positives = 164/337 (48%), Gaps = 21/337 (6%)

Query: 13  DAQLQQLDPLMIEIAGRLNRQPPQVAMTVARGSSDHAASYFAYLTMQHVGIPVASLPMSV 72
           DA    L P  + +   L+    +    VA G++ +A S   Y   Q  G+P      S 
Sbjct: 265 DALRHYLTPEGVNLPAELDFSGLERLTLVACGTAFYACSVAKYWFEQLAGLPCEIDVASE 324

Query: 73  VTMQQAPLKVSGQAVFAFSQSGQSPDLVNSLRLLRKRGALSISMVNAENSPLEAACEFSL 132
              ++ PL     A+F  SQSG++ D + +LR   ++   +I++VN  +S +   C+ +L
Sbjct: 325 FRYREPPLPAKSYAIFV-SQSGETADTLAALRYCTEKVQKTIAVVNVPSSSIARECDLAL 383

Query: 133 PLCAGTESSVAATKSFIATLSASARLIAYWKQDPELLQAGL---------ALPEGLRDAA 183
           P+ AG E  VA+TK+F   L   A +      D   L A           ALP GL +AA
Sbjct: 384 PILAGVEVGVASTKAFTCQLLVLAVMALKAGIDRGHLSADQVQGHLDTLRALP-GLMNAA 442

Query: 184 ---TQDWSLAVDVLRDCQRLMVIGRGAGFAIAQEAALKLKETSAIQAEAFSSAEVKHGPM 240
              + D +   + L + Q ++ +GRG  F +A E ALKLKE S I AE ++S E+KHGP+
Sbjct: 443 LTTSNDIAKLAERLAEAQDILFLGRGPMFPLALEGALKLKEISYIHAEGYASGELKHGPI 502

Query: 241 ALIDDNYPLLVFAPRGAEQAGLLSLAAEMRQRGARVLL------AAPDDVSERDLTLSRA 294
           ALID   P++V AP        +S   E+  R  +VLL       A  + +   L L   
Sbjct: 503 ALIDRLVPVIVLAPHDRLFDKTVSNMQEVMARHGKVLLITDSKGIAAAEGTWAQLRLPEV 562

Query: 295 EHPALDPILAIQSFYVMAAGLAVARGMDPDQPRHLSK 331
             P   PIL      ++A   A+A+G D DQPR+L+K
Sbjct: 563 AEP-FAPILYALPAQLLAYHTAIAKGTDVDQPRNLAK 598


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: 420
Number of extensions: 25
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: 603
Length adjustment: 33
Effective length of query: 303
Effective length of database: 570
Effective search space:   172710
Effective search space used:   172710
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