GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Lactobacillus silagei IWT126

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_089136501.1 CES79_RS04995 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_002217945.1:WP_089136501.1
          Length = 605

 Score =  105 bits (263), Expect = 2e-27
 Identities = 81/263 (30%), Positives = 137/263 (52%), Gaps = 13/263 (4%)

Query: 82  VSGQAVFAF-SQSGQSPDLVNSLRLLRKRGALSISMVNAENSPLEAACEFSLPLCAGTES 140
           +S +  F F SQSG++ D    L  +   G  S+++ N +NS L     ++L L AG E 
Sbjct: 338 LSKKPFFIFLSQSGETADSREVLVNVNAGGYESLTITNVQNSTLSREATYTLLLHAGPEI 397

Query: 141 SVAATKSFIATLSASARLI-AYWKQDPELL--------QAGLALP--EGLRDAATQDWSL 189
           +VA+TK++ A ++  A L  A  + D +++        Q GL     + L D  ++   L
Sbjct: 398 AVASTKAYTAQIAIEAILAKALGEADNQIVAQRFDVRHQLGLVATGMQALVDEKSKIEKL 457

Query: 190 AVDVLRDCQRLMVIGRGAGFAIAQEAALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPL 249
           A            IGRG  ++++ EAALKLKE S +QAE F+S E+KHG +ALI+   P+
Sbjct: 458 AKASFLKTPNAFYIGRGIDWSVSLEAALKLKEISYVQAEGFASGELKHGTIALIEKGTPV 517

Query: 250 LVFAPRGAEQAGLLSLAAEMRQRGARVLLAAPDDVSERDLTLSRAE-HPALDPILAIQSF 308
           +    +        S   E   RGA++L    + +++   TL   +  P + P+L++   
Sbjct: 518 IGIITQEKTAGLTRSNLQETMARGAQILTIVSESLAKPGDTLILPDVDPLMSPLLSVVPT 577

Query: 309 YVMAAGLAVARGMDPDQPRHLSK 331
            ++A   ++ +G+D D+PR+L+K
Sbjct: 578 QLIAYYTSLNKGLDVDKPRNLAK 600


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: 366
Number of extensions: 17
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: 605
Length adjustment: 33
Effective length of query: 303
Effective length of database: 572
Effective search space:   173316
Effective search space used:   173316
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