GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF' in Klebsiella michiganensis M5al

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease

Query= uniprot:A8LLL5
         (334 letters)



>FitnessBrowser__Koxy:BWI76_RS03135
          Length = 290

 Score =  128 bits (321), Expect = 2e-34
 Identities = 84/270 (31%), Positives = 147/270 (54%), Gaps = 15/270 (5%)

Query: 53  PWIFLFPALFVLLLYLGYPVVETLRLSLLE-RVPGGGYQWVGLDNYAQMASEPKFWEAMR 111
           PW+ L P+L  LLL+  +P+  ++  SL + R+   G Q+VGL+N++++ ++  FW+++ 
Sbjct: 7   PWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSVFWQSLV 66

Query: 112 NNMFWLI--VVPALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDG 169
           NN+ +++  VVP ++ A  LLA  LT+  +     ++  F PM I  V A+ +W  ++  
Sbjct: 67  NNLLYILLTVVPGVTLAL-LLAVALTENHRVNRWLRTAFFFPMIIPMVSAAALWLFIF-- 123

Query: 170 RPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVL--VWVQTGFAMVILSAALRG 227
                  +G+L+  +  L G P+    +   N+  L + L  VW   G+ M+   A L+ 
Sbjct: 124 ----MPGLGLLDHYLAKLFG-PMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQS 178

Query: 228 IPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWE- 286
           IP  T EAAI++GA+  Q+FFK+ +P + PT+  V TT  +  +   D V  MT G  + 
Sbjct: 179 IPASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTRGGPDN 238

Query: 287 -TQVLANYMFDKLFRANDWGVGSASAMVIM 315
            T VL  Y+ +  +  +D G  SA+  + +
Sbjct: 239 ATTVLLYYIQNLAWDTHDLGKASAATFLTL 268


Lambda     K      H
   0.329    0.143    0.455 

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: 232
Number of extensions: 16
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: 334
Length of database: 290
Length adjustment: 27
Effective length of query: 307
Effective length of database: 263
Effective search space:    80741
Effective search space used:    80741
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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