GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoP in Klebsiella michiganensis M5al

Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter

Query= TCDB::Q8XEV7
         (438 letters)



>FitnessBrowser__Koxy:BWI76_RS23685
          Length = 444

 Score =  333 bits (855), Expect = 5e-96
 Identities = 179/416 (43%), Positives = 261/416 (62%), Gaps = 6/416 (1%)

Query: 13  YLNKTPLFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIA 72
           YL  TP  QF+L+ CLF LWG A  LNDILI QFK  F L++  +ALVQS F+ GYF +A
Sbjct: 24  YLPHTPWLQFLLVCCLFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVA 83

Query: 73  IPASLVIKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAA 132
           +PA+ +IK+ SYK AI+IGL LY +GC LF PA+ + TY  FLA +  IA GLSFLET+A
Sbjct: 84  LPAAALIKRYSYKAAIIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSA 143

Query: 133 NTYSSMIGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHN 192
           NTYSS++GP   +T R+N SQ F  +G  +G+L+G+ +VF E +   +Q+  M A     
Sbjct: 144 NTYSSLLGPIQSSTQRINFSQIFNSLGVISGVLIGQVMVFGENDPSHEQLLAMPAAAADA 203

Query: 193 FKVLMLENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRP--SALDTLRYLASN 250
            +  M+   + PY  +  VLVV+ ++F+  +FP+CK   +   + P  S   TL+ L + 
Sbjct: 204 ARHQMVGQVVGPYLIIGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAI 263

Query: 251 ARFRRGIVAQFLYVGMQVAVWSFTIR-LALELGDINERDASTFMVYSFACFFIGKFIANI 309
            RFR GI++QFLYVG QV VWSFTIR + L     +E  A+ +++ S   + +GK +A  
Sbjct: 264 PRFRLGILSQFLYVGAQVGVWSFTIRFVQLVQQGTSEHSATYWLLASLVIYAVGKTVATW 323

Query: 310 LMTRFNPEKVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVD 369
           LM R NP  +L  +++   + L     + S  AVY  +LVS    PCW T +   +  + 
Sbjct: 324 LMNRLNPALLLGTFALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMG 383

Query: 370 NEHTEMAGAVIVMAIVGAAVVPAIQGYVADM-FHSLQLSFLVSMLCFVYVGVY-FW 423
            + T+ AG+++VM+I+G AV+P + G ++DM   ++Q++F+  +LCFVYV  Y FW
Sbjct: 384 KD-TQTAGSIVVMSIIGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFYGFW 438


Lambda     K      H
   0.329    0.139    0.412 

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: 464
Number of extensions: 31
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: 438
Length of database: 444
Length adjustment: 32
Effective length of query: 406
Effective length of database: 412
Effective search space:   167272
Effective search space used:   167272
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: 51 (24.3 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