GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Klebsiella michiganensis M5al

Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate BWI76_RS26300 BWI76_RS26300 glycerol-3-phosphate transporter permease

Query= reanno::Smeli:SM_b21653
         (298 letters)



>FitnessBrowser__Koxy:BWI76_RS26300
          Length = 295

 Score =  113 bits (283), Expect = 5e-30
 Identities = 84/279 (30%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 17  WLFVAPALGLITLFMVYPIAWSLWMSFQSGR--GMTLKFAGFANIVRLWNDPVFIKALTN 74
           +L VAP L +  +F ++P   +LW S QS    G++ +F G  N + L+ DP ++ +   
Sbjct: 15  YLLVAPQLVITVIFFIWPAGEALWYSLQSVDPFGLSSQFVGLDNFLALFQDPYYLDSFWT 74

Query: 75  TMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATD 134
           T+ +  +     +L++L  A+L++   + G   ++T + LP   +    +VL+  +F   
Sbjct: 75  TIKFSTMVTVSGLLISLFFAALVDYV-VRGSRFYQTLMLLPYAVAPAVAAVLWIFLFNPG 133

Query: 135 -GIVNSTLQAIGLAASPIPW--LTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSI 191
            G++   L  +G       W    +   A  LV+ A  W+   YN +F+ AALQ+I +S+
Sbjct: 134 RGLITHLLGEMGY-----DWNHAQNSGQAMFLVVFASVWKQISYNFLFFFAALQSIPRSL 188

Query: 192 YEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATL 251
            E A IDG     R   L +PL+ PV  F  V++ +        V +   G GGP  AT 
Sbjct: 189 VEAAAIDGAGPVRRFFRLALPLIAPVSFFLLVVNLVYAFFDTFPVIDAATG-GGPVQATT 247

Query: 252 TLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQF 290
           TL   IY   F  + +L  +A  S V++ LV +L  VQF
Sbjct: 248 TLIYKIYREGFAGL-DLSASAAQSVVLMFLVIILTVVQF 285


Lambda     K      H
   0.330    0.142    0.447 

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: 243
Number of extensions: 14
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: 298
Length of database: 295
Length adjustment: 26
Effective length of query: 272
Effective length of database: 269
Effective search space:    73168
Effective search space used:    73168
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 (21.9 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