GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Klebsiella michiganensis M5al

Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate BWI76_RS18995 BWI76_RS18995 NAD-dependent epimerase

Query= SwissProt::A0R5C5
         (313 letters)



>FitnessBrowser__Koxy:BWI76_RS18995
          Length = 334

 Score =  146 bits (369), Expect = 6e-40
 Identities = 105/333 (31%), Positives = 163/333 (48%), Gaps = 28/333 (8%)

Query: 1   MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSGRAENLHSAE----NSDKFEFVKAD 56
           M+ LVTGAAGFIG     RLL  GH VVGLD+++     NL  A      S  F F K D
Sbjct: 1   MKFLVTGAAGFIGFHTCKRLLEAGHEVVGLDNMNDYYDVNLKQARLDLLQSPLFSFHKID 60

Query: 57  IVDAD-LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVRK 115
           + D + +  L A  K   + HLAAQ  V+ S+++P   A  N++G + + E  R   V  
Sbjct: 61  LADREGIARLFANEKFNRVIHLAAQAGVRYSLENPFAYADANLIGYLNILEGCRHNNVEH 120

Query: 116 VVHTSSGGSVYGTPPAYPTSEDMPV-NPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAPA 174
           +++ SS  SVYG     P S D  V +P S YAA K A E+  + Y +LY +  + +   
Sbjct: 121 LLYASS-SSVYGLNRKMPFSTDDSVDHPVSLYAATKKANELMAHTYSHLYGIPTTGLRFF 179

Query: 175 NVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVR------- 227
            VYGP   P      +  F++A+L G+   ++  G   RD+ ++DD+V+A VR       
Sbjct: 180 TVYGPWGRPD---MALFKFTKAMLEGKPIDVYNYGKMKRDFTYIDDIVEAIVRMQDIIPQ 236

Query: 228 --------AGGPAGGG---QRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDLR 276
                    G PA      + +N+G        +  TA+  A+G   E    P + GD+ 
Sbjct: 237 PNPEWTVETGSPADSSAPYRVYNIGNSSPVELMDYITALEEAMGMVAEKNMMPIQPGDVL 296

Query: 277 RSRLDNTRAREVLGWQPQVALAEGIAKTVEFFR 309
            +  D     + +G++PQ  + +G+   V++++
Sbjct: 297 ETSADTKPLYDAVGFRPQTTVRQGVKNFVDWYK 329


Lambda     K      H
   0.317    0.136    0.396 

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: 236
Number of extensions: 12
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: 313
Length of database: 334
Length adjustment: 28
Effective length of query: 285
Effective length of database: 306
Effective search space:    87210
Effective search space used:    87210
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: 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