GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Klebsiella michiganensis M5al

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>FitnessBrowser__Koxy:BWI76_RS03110
          Length = 499

 Score =  387 bits (995), Expect = e-112
 Identities = 210/464 (45%), Positives = 297/464 (64%), Gaps = 9/464 (1%)

Query: 14  SKKLPPLTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTS 73
           +K   P +E P    +  VAL+AT GGLLFGYDTGVI+GAL  M  EL LT FT G+VTS
Sbjct: 10  NKASGPNSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTS 69

Query: 74  SLLFGAAAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAV 133
           SLLFGAA GA+  G +++  GR+K I+ LAV F +G +    AP    M+  R++LG+AV
Sbjct: 70  SLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAV 129

Query: 134 GGASTVVPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYML 193
           GGA+  VPVY+AE+AP   RG L    ELMIV GQL A++ NA    V+G  +  WR+ML
Sbjct: 130 GGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWG-GESTWRWML 188

Query: 194 AIAAIPAIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREE 253
           A+A +PA+ L+FGM+ +P+SPRW   +GR+ EAR VLE  R  +    E+ ++     E+
Sbjct: 189 AVATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHKDDVEWELLEITETLDEQ 248

Query: 254 HAVSEKSMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAAL 313
             + +      EI+ + WL ++ ++GIG+ V QQLTG+N+IMYY   VL   G ++NAAL
Sbjct: 249 RNLGKPRFS--EIM-TPWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNAAL 305

Query: 314 IANVAPGVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFP-----VGD 368
            A +A GV++V+  F+ +WM+ +I RR   + G    T   V IG  S   P       D
Sbjct: 306 FATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPD 365

Query: 369 PLRPYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLF 428
            LR Y++L  +++F+   Q  L+  TW+++SE+FP  +RG  +G +VF +WIAN  + LF
Sbjct: 366 ALRAYMVLAGMLLFLSFQQGALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLF 425

Query: 429 FPTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEID 472
           FP ++  +GL+GTFF+FAGIGV   IF+   VPETR R+LE+I+
Sbjct: 426 FPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQIE 469


Lambda     K      H
   0.327    0.142    0.420 

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: 627
Number of extensions: 25
Number of successful extensions: 5
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: 491
Length of database: 499
Length adjustment: 34
Effective length of query: 457
Effective length of database: 465
Effective search space:   212505
Effective search space used:   212505
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 (21.7 bits)
S2: 52 (24.6 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