GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Klebsiella michiganensis M5al

Align Phospho-furanose lactonase; EC 3.1.1.25 (characterized)
to candidate BWI76_RS14780 BWI76_RS14780 phosphotriesterase

Query= SwissProt::Q4A724
         (353 letters)



>FitnessBrowser__Koxy:BWI76_RS14780
          Length = 323

 Score =  152 bits (385), Expect = 9e-42
 Identities = 104/336 (30%), Positives = 164/336 (48%), Gaps = 32/336 (9%)

Query: 7   RTVLGDIPVEKLGITDCHDHFIKNGGPEVEEHIDFLMLN-VDASIKEFKEFIDRGGSTIV 65
           RT+ GDI   +LG+T  HDH         E   D L+L+   AS +E  +F + GG  I 
Sbjct: 5   RTLNGDISAHQLGVTYSHDHIYCIPPYWAERQDDDLLLDDPQASERELSDFREAGGRAIY 64

Query: 66  TMDPPNVGRDVLKTLEIANAVKNLGGNVIMSTGFHKAKFYDK--------YSSWLAVVPT 117
               P+ GR       +A   +    ++I + GF+K   +          ++ W+     
Sbjct: 65  DATAPDYGRQAAAVAAMAQRQQL---HIIATAGFNKGFLWSSKRPGSAQTFAEWIEHSEI 121

Query: 118 EEIVKMCVAEIEEGMDEYNYNGPVVKRSKAKAGIIKAGTGYGAIDRLELKALEVAARTSI 177
           +E+V+    E+ EG          ++ +  +AG++K GTGY  I  LE K +EV  R   
Sbjct: 122 DELVEHVCREVTEG----------IEGTAHRAGVVKCGTGYNTISPLEEKTMEVIVRAQQ 171

Query: 178 LTGCPILVHTQLGTMALEVAKHLIGFGANPDKIQISHLNKNPDKYYYEKVIKETGVTLCF 237
            TG P+  HT++GTM LE A+    +G +  ++  +H+++NPD + + + I  TG  L F
Sbjct: 172 RTGAPMHSHTEMGTMGLEQARIFKKWGLDLSRLCFAHMDRNPDPWLHRQ-IANTGAFLSF 230

Query: 238 DGPDRVKYYPDSLLAENIKYLVDKGLQKHITLSLDAGRILYQRNYGLTKGKQTFGLAYLF 297
           DG  R+KY+P+ +  + I  L  +G QK I +  D  R     +Y    GK   GL ++ 
Sbjct: 231 DGISRIKYHPEHIRTQAILALCQRGYQKQILIGGDFARKSMSAHY----GKGGLGLKFIL 286

Query: 298 D----RFLPLLKQVGVSKEAIF-DILVNNPKRVLAF 328
           +    RFL   ++ G   EA+  D  V+NP R LAF
Sbjct: 287 NDWRPRFLEEAREAGFDGEALLHDFFVDNPARYLAF 322


Lambda     K      H
   0.319    0.139    0.402 

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: 293
Number of extensions: 22
Number of successful extensions: 6
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: 353
Length of database: 323
Length adjustment: 28
Effective length of query: 325
Effective length of database: 295
Effective search space:    95875
Effective search space used:    95875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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