GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glucosaminate-lyase in Marinobacter adhaerens HP15

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate GFF2122 HP15_2076 secreted protein containing thioredoxin reductase domain

Query= curated2:Q93HX6
         (320 letters)



>FitnessBrowser__Marino:GFF2122
          Length = 317

 Score =  420 bits (1080), Expect = e-122
 Identities = 206/314 (65%), Positives = 249/314 (79%), Gaps = 1/314 (0%)

Query: 1   MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60
           M + +HSR+IILGSGPAGY+AAVYAARANL P LITG++ GGQLTTTT+VDNWPGD  G+
Sbjct: 1   MSDTKHSRLIILGSGPAGYTAAVYAARANLNPTLITGIEVGGQLTTTTDVDNWPGDNDGV 60

Query: 61  TGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYL 120
            GP LM+RM +HAERFET IV+D IN  D   +P+ L GD   YTCD LIIATGASA YL
Sbjct: 61  QGPELMQRMLKHAERFETSIVYDTINEADLRNRPFRLKGDGGEYTCDTLIIATGASAMYL 120

Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180
           GL SEE F G+GVSACATCDGFFY+ + VAV+GGGNTAVEEALYL+NIA  VTL+HRR++
Sbjct: 121 GLESEEKFKGQGVSACATCDGFFYKKQKVAVIGGGNTAVEEALYLSNIADEVTLVHRRDS 180

Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKN-NDGSFDELKVDGVF 239
            RAEKIL DKL  +   G + +  +  LDEVLGD  GVTG R+K+  D S  E+ + GVF
Sbjct: 181 LRAEKILQDKLFEKAENGNVKIVWDHTLDEVLGDGTGVTGMRVKSTKDDSTQEMDLAGVF 240

Query: 240 IAIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299
           IAIGH PNT LF+GQL +++GY+ ++ G +G AT +S+ G+FAAGDVADHVYRQA+TSAG
Sbjct: 241 IAIGHKPNTDLFQGQLDMENGYIRIRSGLEGMATQSSIPGVFAAGDVADHVYRQAVTSAG 300

Query: 300 AGCMAALDTERYLD 313
            GCMAALD E++LD
Sbjct: 301 FGCMAALDAEKFLD 314


Lambda     K      H
   0.318    0.135    0.386 

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: 369
Number of extensions: 13
Number of successful extensions: 2
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: 320
Length of database: 317
Length adjustment: 27
Effective length of query: 293
Effective length of database: 290
Effective search space:    84970
Effective search space used:    84970
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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